| Type: | Package |
| Title: | Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R |
| Version: | 9.7 |
| Date: | 2024-09-30 |
| Maintainer: | Xiaowei Zhan <zhanxw@gmail.com> |
| Description: | Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile. |
| Copyright: | We have used the following software and made minimal necessary changes: tabix, Heng Li <lh3@live.co.uk> (MIT license), SQLite (Public Domain), Zstandard (BSD license). For tabix, we removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics. For zstandard, we removed compiler (clang, MSVC) specific preprocessing flags. |
| License: | GPL-2 | GPL-3 | file LICENSE [expanded from: GPL | file LICENSE] |
| URL: | http://zhanxw.github.io/seqminer/ |
| BugReports: | https://github.com/zhanxw/seqminer/issues |
| Packaged: | 2024-10-02 03:13:09 UTC; zhanxw |
| Repository: | CRAN |
| Suggests: | testthat, SKAT |
| SystemRequirements: | C++17, zlib headers and libraries, GNU make, optionally also bzip2 and POSIX-compliant regex functions. |
| NeedsCompilation: | yes |
| RoxygenNote: | 7.2.3 |
| Encoding: | UTF-8 |
| Author: | Xiaowei Zhan [aut, cre], Dajiang Liu [aut], Attractive Chaos [cph] (We have used the following software and made minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT license). We removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics.), Broad Institute / Massachusetts Institute of Technology [cph], Genome Research Ltd (GRL) [cph], Facebook, Inc [cph], D. Richard Hipp [cph] |
| Date/Publication: | 2024-10-02 06:10:02 UTC |
Efficiently Read Sequencing Data (VCF format, METAL format) into R
Description
SeqMiner provides functions to easily load Variant Call Format (VCF) or METAL format into R
Details
The aim of this package is to save your time parsing large text file. That means data processing time can be saved for other researches. This packages requires Bgzip compressed and Tabix indexed files as input. If input files contaians annotation by TabAnno (), it is possible to extract information at the unit of genes.
Author(s)
Maintainer: Xiaowei Zhan zhanxw@gmail.com
Authors:
Dajiang Liu dajiang.liu@gmail.com
Other contributors:
Attractive Chaos attractor@live.co.uk (We have used the following software and made minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT license). We removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics.) [copyright holder]
Broad Institute / Massachusetts Institute of Technology [copyright holder]
Genome Research Ltd (GRL) [copyright holder]
Facebook, Inc [copyright holder]
D. Richard Hipp [copyright holder]
See Also
Useful links:
Read from binary PLINK file and return a genotype matrix
Description
Read from binary PLINK file and return a genotype matrix
Usage
## S3 method for class 'PlinkFile'
plinkFileObject[sampleIndex, markerIndex]
Arguments
plinkFileObject |
a PlinkFileObject obtained by openPlink() |
sampleIndex |
integer, 1-basd, index of samples to be extracted |
markerIndex |
integer, 1-basd, index of markers to be extracted |
Value
genotype matrix, marker by sample
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
## these indice are nonsynonymous markers for 1:196621007-196716634",
## refer to the readVCFToMatrixByRange()
fileName = system.file("plink/all.anno.filtered.extract.bed", package = "seqminer")
filePrefix = sub(fileName, pattern = ".bed", replacement = "")
plinkObj = openPlink(filePrefix)
sampleIndex = seq(3)
markerIndex =c(14, 36)
cfh <- plinkObj[sampleIndex, markerIndex]
Add a job to a workflow
Description
Add a job to a workflow
Usage
addJob(wf, job)
Arguments
wf |
a variable of workflow class |
job |
a variable of job class |
Examples
j1 <- newJob('id1', 'cmd out1', 'out1')
j2 <- newJob('id2', 'cmd out2', 'out2', depend = 'out1')
w <- newWorkflow("wf")
w <- addJob(w, j1)
w <- addJob(w, j2)
outFile <- file.path(tempdir(), "Makefile")
writeWorkflow(w, outFile)
cat('Outputted Makefile file are in the temp directory:', outFile, '\n')
Annotate a test variant
Description
Annotate a test variant
Usage
annotateGene(param, chrom, position, ref, alt)
Arguments
param |
a list of annotation configuaration (e.g. reference file, gene definition) |
chrom |
a vector of chromosome names |
position |
a vector of chromosome positions |
ref |
a vector of reference alleles |
alt |
a vector of alternative alleles |
Value
annotated results in a data frame structure
See Also
makeAnnotationParameter
Examples
if (.Platform$endian == "little") {
param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
param <- makeAnnotationParameter(param)
print(param)
annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
} else {
message("Tabix does not work well for big endian for now")
}
Annotate a plain text file
Description
Annotate a plain text file
Usage
annotatePlain(inFile, outFile, params)
Arguments
inFile |
input file name |
outFile |
output file name |
params |
parameters |
Value
0 if succeed
Examples
param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"),
inputFormat = "plain")
param <- makeAnnotationParameter(param)
inFile <- system.file("tabanno/input.test.plain.txt", package = "seqminer")
outFile <- file.path(tempdir(), "out.annotated.txt")
annotatePlain(inFile, outFile, param)
cat('Outputted annotation results are in the temp directory:', outFile, '\n')
Annotate a VCF file
Description
Annotate a VCF file
Usage
annotateVcf(inVcf, outVcf, params)
Arguments
inVcf |
input VCF file name |
outVcf |
output VCF file name |
params |
parameters |
Value
0 if succeed
Examples
param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
param <- makeAnnotationParameter(param)
inVcf <- system.file("tabanno/input.test.vcf", package = "seqminer")
outVcf <- file.path(tempdir(), "/", "out.vcf")
annotateVcf (inVcf, outVcf, param)
cat('Annotated VCF files are in the temp directory:', outVcf, '\n')
Create a single chromosome index
Description
Create a single chromosome index
Usage
createSingleChromosomeBCFIndex(fileName, indexFileName = NULL)
Arguments
fileName |
character, represents an input BCF file (Bgzipped, with Tabix index) |
indexFileName |
character, by default, create 'fileName'.scIdx |
Value
indexFileName if success, or NULL is failed
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.headerFixed.bcf.gz", package = "seqminer")
cfh <- createSingleChromosomeBCFIndex(fileName)
Create a single chromosome index
Description
Create a single chromosome index
Usage
createSingleChromosomeVCFIndex(fileName, indexFileName = NULL)
Arguments
fileName |
character, represents an input VCF file (Bgzipped, with Tabix index) |
indexFileName |
character, by default, create 'fileName'.scIdx |
Value
indexFileName if success, or NULL is failed
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
cfh <- createSingleChromosomeVCFIndex(fileName)
Download annotation resources to a directory
Description
Download annotation resources to a directory
Usage
download.annotation.resource(outputDirectory)
Arguments
outputDirectory |
the directory to store annotation resources |
Value
will not return anything
Examples
## Not run:
download.annotation.resource("/tmp")
## End(Not run)
Extract pair of positions by ranges
Description
Extract pair of positions by ranges
Usage
getCovPair(covData, rangeList1, rangeList2)
Arguments
covData |
a covariance matrix with positions as dimnames |
rangeList1 |
character specify a range, 1-based index |
rangeList2 |
character specify a range, 1-based index |
Value
a covariance matrix covFileName = system.file("rvtests/rvtest.MetaCov.assoc.gz", package = "seqminer") cfh <- rvmeta.readCovByRange(covFileName, "1:196621007-196716634") rangeList1 <- "1:196621007-196700000" rangeList2 <- "1:196700000-196716634" getCovPair(cfh, rangeList1, rangeList2)
Annotate a test variant
Description
Annotate a test variant
Usage
getRefBase(reference, chrom, position, len = NULL)
Arguments
reference |
path to the reference genome file (.fa file) |
chrom |
a vector of chromosome names |
position |
a vector of chromosome positions |
len |
a vector of length |
Value
based extracted from the reference genome
Check input file has tabix index
Description
Check input file has tabix index
Usage
hasIndex(fileName)
Arguments
fileName |
character vector, representing file names an input file name |
Value
TRUE if an index file with ".tbi" or "bci" exists, and created later than VCF/BCF file
Test whether directory is writable
Description
Test whether directory is writable
Usage
isDirWritable(outDir)
Arguments
outDir |
the name of the directory |
Value
TRUE if the file is writable isDirWritable("~")
Test whether a vector of positions are inside given ranges
Description
Test whether a vector of positions are inside given ranges
Usage
isInRange(positions, rangeList)
Arguments
positions |
characters, positions. e.g. c("1:2-3", "1:4") |
rangeList |
character, ranges, e.g. "1:1-3,1:2-4", 1-based index |
Value
logical vector, TRUE/FALSE/NA
Examples
positions <- c("1:2-3", "1:4", "XX")
ranges <- "1:1-3,1:2-4,1:5-10"
isInRange(positions, ranges)
Check if the inputs are valid tabix range such as chr1:2-300
Description
Check if the inputs are valid tabix range such as chr1:2-300
Usage
isTabixRange(range)
Arguments
range |
characer vector |
Examples
valid <- isTabixRange(c("chr1:1-200", "X:1", "1:100-100", "chr1", "1:1-20,1:30-40"))
stopifnot(all(valid))
invalid <- isTabixRange(c(":1", "chr1::", ":-"))
stopifnot(all(!invalid))
Check if the input is url e.g. http:// or ftp://
Description
Check if the input is url e.g. http:// or ftp://
Usage
isURL(fileName)
Arguments
fileName |
character vector |
Construct a usable set of annotation parameters
Description
Construct a usable set of annotation parameters
Usage
makeAnnotationParameter(param = NULL)
Arguments
param |
a list of annotation elements |
Value
list, a complete list of supported parameters
Create a new job
Description
Create a new job
Usage
newJob(id, cmd, outFile, depend = NULL)
Arguments
id |
character, job ids. |
cmd |
character, commands to run |
outFile |
character, the output file names after command are run successfully |
depend |
character vector, specify the prerequisite files (e.g. outFile from other jobs) |
Examples
j1 <- newJob('id1', 'cmd out1', 'out1')
j2 <- newJob('id2', 'cmd out2', 'out2', depend = 'out1')
Create a new workflow
Description
Create a new workflow
Usage
newWorkflow(name)
Arguments
name |
character, specify the name of the workflow |
Examples
w <- newWorkflow("wf")
Open binary PLINK files
Description
Open binary PLINK files
Usage
openPlink(fileName)
Arguments
fileName |
character, represents the prefix of PLINK input file |
Value
an PLINK file object with class name ("PlinkFile")
Examples
fileName = system.file("plink/all.anno.filtered.extract.bed", package = "seqminer")
fileName = sub(fileName, pattern = ".bed", replacement = "")
plinkObj <- openPlink(fileName)
str(plinkObj)
Read information from BGEN file in a given range and return a list
Description
Read information from BGEN file in a given range and return a list
Usage
readBGENToListByGene(fileName, geneFile, geneName)
Arguments
fileName |
character, represents an input BGEN file (Bgzipped, with Tabix index) |
geneFile |
character, a text file listing all genes in refFlat format |
geneName |
character vector, which gene(s) to be extracted |
Value
a list of chrom, pos, varid, rsid, alleles, isPhased, probability, sampleId
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("bgen/all.anno.filtered.extract.bgen", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- readBGENToListByGene(fileName, geneFile, "CFH")
Read information from BGEN file in a given range and return a list
Description
Read information from BGEN file in a given range and return a list
Usage
readBGENToListByRange(fileName, range)
Arguments
fileName |
character, represents an input BGEN file (Bgzipped, with Tabix index) |
range |
character, a text indicating which range in the BGEN file to extract. e.g. 1:100-200, 1-based index |
Value
a list of chrom, pos, varid, rsid, alleles, isPhased, probability, sampleId
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("bgen/all.anno.filtered.extract.bgen", package = "seqminer")
cfh <- readBGENToListByRange(fileName, "1:196621007-196716634")
Read a gene from BGEN file and return a genotype matrix
Description
Read a gene from BGEN file and return a genotype matrix
Usage
readBGENToMatrixByGene(fileName, geneFile, geneName)
Arguments
fileName |
character, represents an input BGEN file (Bgzipped, with Tabix index) |
geneFile |
character, a text file listing all genes in refFlat format |
geneName |
character vector, which gene(s) to be extracted |
Value
genotype matrix
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("bgen/all.anno.filtered.extract.bgen", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- readBGENToMatrixByGene(fileName, geneFile, "CFH")
Read a gene from BGEN file and return a genotype matrix
Description
Read a gene from BGEN file and return a genotype matrix
Usage
readBGENToMatrixByRange(fileName, range)
Arguments
fileName |
character, represents an input BGEN file (Bgzipped, with Tabix index) |
range |
character, a text indicating which range in the BGEN file to extract. e.g. 1:100-200, 1-based index |
Value
genotype matrix
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("bgen/all.anno.filtered.extract.bgen", package = "seqminer")
cfh <- readBGENToMatrixByRange(fileName, "1:196621007-196716634")
Read from binary PLINK file and return a genotype matrix
Description
Read from binary PLINK file and return a genotype matrix
Usage
readPlinkToMatrixByIndex(plinkFilePrefix, sampleIndex, markerIndex)
Arguments
plinkFilePrefix |
a PlinkFileObject obtained by openPlink() |
sampleIndex |
integer, 1-basd, index of samples to be extracted |
markerIndex |
integer, 1-basd, index of markers to be extracted |
Value
genotype matrix, marker by sample
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
## these indice are nonsynonymous markers for 1:196621007-196716634",
## refer to the readVCFToMatrixByRange()
fileName = system.file("plink/all.anno.filtered.extract.bed", package = "seqminer")
fileName = sub(fileName, pattern = ".bed", replacement = "")
sampleIndex = seq(3)
markerIndex =c(14, 36)
cfh <- readPlinkToMatrixByIndex(fileName, sampleIndex, markerIndex)
Read a range from BCF file and return a genotype matrix
Description
Read a range from BCF file and return a genotype matrix
Usage
readSingleChromosomeBCFToMatrixByRange(fileName, range, indexFileName = NULL)
Arguments
fileName |
character, represents an input BCF file (Bgzipped, with Tabix index) |
range |
character, a text indicating which range in the BCF file to extract. e.g. 1:100-200, 1-based index |
indexFileName |
character, index file, by default, it s 'fileName'.scIdx |
Value
genotype matrix
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.headerFixed.bcf.gz", package = "seqminer")
cfh <- readSingleChromosomeBCFToMatrixByRange(fileName, "1:196621007-196716634")
Read a range from VCF file and return a genotype matrix
Description
Read a range from VCF file and return a genotype matrix
Usage
readSingleChromosomeVCFToMatrixByRange(fileName, range, indexFileName = NULL)
Arguments
fileName |
character, represents an input VCF file (Bgzipped, with Tabix index) |
range |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index |
indexFileName |
character, index file, by default, it s 'fileName'.scIdx |
Value
genotype matrix
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
cfh <- readSingleChromosomeVCFToMatrixByRange(fileName, "1:196621007-196716634")
Read information from VCF file in a given range and return a list
Description
Read information from VCF file in a given range and return a list
Usage
readVCFToListByGene(
fileName,
geneFile,
geneName,
annoType,
vcfColumn,
vcfInfo,
vcfIndv
)
Arguments
fileName |
character, represents an input VCF file (Bgzipped, with Tabix index) |
geneFile |
character, a text file listing all genes in refFlat format |
geneName |
character vector, which gene(s) to be extracted |
annoType |
character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty. |
vcfColumn |
character vector, which vcf columns to extract. It can be chosen from CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT and etc. |
vcfInfo |
character vector, which should be tags in the INFO columns to extarct. Common choices include: DP, AC, AF, NS |
vcfIndv |
character vector, which values to extract at individual level. Common choices are: GT, GQ, GD |
Value
a list of genes, and each elements has specified vcfColumn, vcfinfo, vcfIndv
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- readVCFToListByGene(fileName, geneFile, "CFH", "Synonymous",
c("CHROM", "POS"), c("AF", "AC"), c("GT") )
Read information from VCF file in a given range and return a list
Description
Read information from VCF file in a given range and return a list
Usage
readVCFToListByRange(fileName, range, annoType, vcfColumn, vcfInfo, vcfIndv)
Arguments
fileName |
character, represents an input VCF file (Bgzipped, with Tabix index) |
range |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index |
annoType |
character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty. |
vcfColumn |
character vector, which vcf columns to extract. It can be chosen from CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT and etc. |
vcfInfo |
character vector, which should be tags in the INFO columns to extarct. Common choices include: DP, AC, AF, NS |
vcfIndv |
character vector, which values to extract at individual level. Common choices are: GT, GQ, GD |
Value
a list of genes, and each elements has specified vcfColumn, vcfinfo, vcfIndv
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
cfh <- readVCFToListByRange(fileName, "1:196621007-196716634", "Nonsynonymous",
c("CHROM", "POS"), c("AF", "AC"), c("GT") )
Read a gene from VCF file and return a genotype matrix
Description
Read a gene from VCF file and return a genotype matrix
Usage
readVCFToMatrixByGene(fileName, geneFile, geneName, annoType)
Arguments
fileName |
character, represents an input VCF file (Bgzipped, with Tabix index) |
geneFile |
character, a text file listing all genes in refFlat format |
geneName |
character vector, which gene(s) to be extracted |
annoType |
character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty. |
Value
genotype matrix
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- readVCFToMatrixByGene(fileName, geneFile, "CFH", "Synonymous")
Read a gene from VCF file and return a genotype matrix
Description
Read a gene from VCF file and return a genotype matrix
Usage
readVCFToMatrixByRange(fileName, range, annoType)
Arguments
fileName |
character, represents an input VCF file (Bgzipped, with Tabix index) |
range |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index |
annoType |
character, annotated types you would like to extract, such as "Nonsynonymous", "Synonymous". This can be left empty. |
Value
genotype matrix
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
cfh <- readVCFToMatrixByRange(fileName, "1:196621007-196716634", "Nonsynonymous")
Read covariance by range from METAL-format files.
Description
Read covariance by range from METAL-format files.
Usage
rvmeta.readCovByRange(covFile, tabixRange)
Arguments
covFile |
character, a covariance file (rvtests outputs using –meta cov) |
tabixRange |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200 |
Value
a matrix of covariance within given range
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
covFileName = system.file("rvtests/rvtest.MetaCov.assoc.gz", package = "seqminer")
cfh <- rvmeta.readCovByRange(covFileName, "1:196621007-196716634")
Read association statistics by gene from METAL-format files. Both score statistics and covariance statistics will be extracted.
Description
Read association statistics by gene from METAL-format files. Both score statistics and covariance statistics will be extracted.
Usage
rvmeta.readDataByGene(
scoreTestFiles,
covFiles,
geneFile,
geneName,
multiAllelic = FALSE
)
Arguments
scoreTestFiles |
character vector, score test output files (rvtests outputs using –meta score) |
covFiles |
character vector, covaraite files (rvtests outputs using –meta cov) |
geneFile |
character, a text file listing all genes in refFlat format |
geneName |
character vector, which gene(s) to be extracted |
multiAllelic |
boolean, whether to read multi-allelic sites as multiple variants or not |
Value
a list of statistics including chromosome, position, allele frequency, score statistics, covariance and annotation(if input files are annotated).
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
scoreFileName = system.file("rvtests/rvtest.MetaScore.assoc.anno.gz", package = "seqminer")
covFileName = system.file("rvtests/rvtest.MetaCov.assoc.gz", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- rvmeta.readDataByGene(scoreFileName, covFileName, geneFile, "CFH")
Read association statistics by range from METAL-format files. Both score statistics and covariance statistics will be extracted.
Description
Read association statistics by range from METAL-format files. Both score statistics and covariance statistics will be extracted.
Usage
rvmeta.readDataByRange(scoreTestFiles, covFiles, ranges, multiAllelic = FALSE)
Arguments
scoreTestFiles |
character vector, score test output files (rvtests outputs using –meta score) |
covFiles |
character vector, covaraite files (rvtests outputs using –meta cov) |
ranges |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200, 1-based index |
multiAllelic |
boolean, whether to read multi-allelic sites as multiple variants or not |
Value
a list of statistics including chromosome, position, allele frequency, score statistics, covariance and annotation(if input files are annotated).
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
scoreFileName = system.file("rvtests/rvtest.MetaScore.assoc.anno.gz", package = "seqminer")
covFileName = system.file("rvtests/rvtest.MetaCov.assoc.gz", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- rvmeta.readDataByRange(scoreFileName, covFileName, "1:196621007-196716634")
Read null model statistics
Description
Read null model statistics
Usage
rvmeta.readNullModel(scoreTestFiles)
Arguments
scoreTestFiles |
character vector, score test output files (rvtests outputs using –meta score) |
Value
a list of statistics fitted under the null mode (without genetic effects)
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
scoreFileName = system.file("rvtests/rvtest.MetaScore.assoc.anno.gz", package = "seqminer")
Read score test statistics by range from METAL-format files.
Description
Read score test statistics by range from METAL-format files.
Usage
rvmeta.readScoreByRange(scoreTestFiles, tabixRange)
Arguments
scoreTestFiles |
character vector, score test output files (rvtests outputs using –meta score) |
tabixRange |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200 |
Value
score test statistics within given range
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
scoreFileName = system.file("rvtests/rvtest.MetaScore.assoc.anno.gz", package = "seqminer")
cfh <- rvmeta.readScoreByRange(scoreFileName, "1:196621007-196716634")
Read skew by range from METAL-format files.
Description
Read skew by range from METAL-format files.
Usage
rvmeta.readSkewByRange(skewFile, tabixRange)
Arguments
skewFile |
character, a skew file (rvtests outputs using –meta skew) |
tabixRange |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200 |
Value
an 3-dimensional array of skewness within given range
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
skewFileName = system.file("rvtests/rvtest.MetaSkew.assoc.gz", package = "seqminer")
cfh <- rvmeta.readSkewByRange(skewFileName, "1:196621007-196716634")
Write covariance association statistics files.
Description
Write covariance association statistics files.
Usage
rvmeta.writeCovData(rvmetaData, outName)
Arguments
rvmetaData |
a list vector. It's usually read by rvmeta.readDataByRange or rvmeta.readDataByGene function |
outName |
character, a text indicating output file prefix |
Value
TRUE only if succeed
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
scoreFileName = system.file("rvtests/rvtest.MetaScore.assoc.anno.gz", package = "seqminer")
covFileName = system.file("rvtests/rvtest.MetaCov.assoc.gz", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- rvmeta.readDataByRange(scoreFileName, covFileName, "1:196621007-196716634")
outFile <- file.path(tempdir(), "cfh.MetaCov.assoc.gz")
rvmeta.writeCovData(cfh, outFile)
cat('Outputted MetaCov file are in the temp directory:', outFile, '\n')
Write score-based association statistics files.
Description
Write score-based association statistics files.
Usage
rvmeta.writeScoreData(rvmetaData, outName, createIndex = FALSE)
Arguments
rvmetaData |
a list vector. It's usually read by rvmeta.readDataByRange or rvmeta.readDataByGene function |
outName |
character, a text indicating output file prefix |
createIndex |
boolean, (default FALSE), whether or not to create the index |
Value
TRUE only if succeed
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
scoreFileName = system.file("rvtests/rvtest.MetaScore.assoc.anno.gz", package = "seqminer")
covFileName = system.file("rvtests/rvtest.MetaCov.assoc.gz", package = "seqminer")
geneFile = system.file("vcf/refFlat_hg19_6col.txt.gz", package = "seqminer")
cfh <- rvmeta.readDataByRange(scoreFileName, covFileName, "1:196621007-196716634")
outFile <- file.path(tempdir(), "cfh.MetaScore.assoc")
rvmeta.writeScoreData(cfh, outFile)
cat('Outputted MetaScore file are in the temp directory:', outFile, '\n')
Create tabix index file, similar to running tabix in command line.
Description
Create tabix index file, similar to running tabix in command line.
Usage
tabix.createIndex(
bgzipFile,
sequenceColumn = 1,
startColumn = 4,
endColumn = 5,
metaChar = "#",
skipLines = 0
)
Arguments
bgzipFile |
character, an tabix indexed file |
sequenceColumn |
integer, sequence name column |
startColumn |
integer, start column |
endColumn |
integer, end column |
metaChar |
character, symbol for comment/meta lines |
skipLines |
integer, first this number of lines will be skipped |
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
tabix.createIndex(fileName, 1, 2, 0, '#', 0)
Create tabix index for bgzipped MetaScore/MetaCov file
Description
Create tabix index for bgzipped MetaScore/MetaCov file
Usage
tabix.createIndex.meta(bgzipFile)
Arguments
bgzipFile |
character, input vcf file |
See Also
http://zhanxw.com/seqminer/ for online manual and examples
http://zhanxw.github.io/rvtests/ for rvtests
Examples
fileName = system.file("rvtests/rvtest.MetaScore.assoc.anno.gz", package = "seqminer")
tabix.createIndex.meta(fileName)
Create tabix index for bgzipped VCF file
Description
Create tabix index for bgzipped VCF file
Usage
tabix.createIndex.vcf(bgzipVcfFile)
Arguments
bgzipVcfFile |
character, input vcf file |
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
tabix.createIndex.vcf(fileName)
Read tabix file, similar to running tabix in command line.
Description
Read tabix file, similar to running tabix in command line.
Usage
tabix.read(tabixFile, tabixRange)
Arguments
tabixFile |
character, an tabix indexed file |
tabixRange |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200 |
Value
character vector, each elements is an individual line
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
if (.Platform$endian == "little") {
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
snp <- tabix.read(fileName, "1:196623337-196632470")
} else {
message("Tabix does not work well for big endian for now")
}
Read tabix file, similar to running tabix in command line.
Description
Read tabix file, similar to running tabix in command line.
Usage
tabix.read.header(tabixFile, skippedLine = FALSE)
Arguments
tabixFile |
character, an tabix indexed file |
skippedLine |
logical, whether to read tabix skipped lines (when used 'tabix -S NUM') |
Value
a list
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
snp <- tabix.read.header(fileName)
Read tabix file, similar to running tabix in command line.
Description
Read tabix file, similar to running tabix in command line.
Usage
tabix.read.table(
tabixFile,
tabixRange,
col.names = TRUE,
stringsAsFactors = FALSE
)
Arguments
tabixFile |
character, an tabix indexed file |
tabixRange |
character, a text indicating which range in the VCF file to extract. e.g. 1:100-200 |
col.names |
logical, use tabix file header as result headers (default: TRUE) |
stringsAsFactors |
logical, store loaded data as factors (default: FALSE) |
Value
data frame, each elements is an individual line
See Also
http://zhanxw.com/seqminer/ for online manual and examples
Examples
fileName = system.file("vcf/all.anno.filtered.extract.vcf.gz", package = "seqminer")
snp <- tabix.read.table(fileName, "1:196623337-196632470")
Validate annotate parameter is valid
Description
Validate annotate parameter is valid
Usage
validateAnnotationParameter(param, debug = FALSE)
Arguments
param |
a list of annotation elements |
debug |
show extra debug information or not |
Value
list, first element is TRUE/FALSE if parameter is valid/invalid;
validate the inVcf can be created, and outVcf can be write to. will stop if any error occurs
Description
validate the inVcf can be created, and outVcf can be write to. will stop if any error occurs
Usage
verifyFilename(inVcf, outVcf)
Arguments
inVcf |
input file |
outVcf |
output file |
Export workflow to Makefile
Description
Export workflow to Makefile
Usage
writeWorkflow(wf, outFile)
Arguments
wf |
a variable workflow class |
outFile |
character, typically named "Makefile" |
Examples
j1 <- newJob('id1', 'cmd out1', 'out1')
j2 <- newJob('id2', 'cmd out2', 'out2', depend = 'out1')
w <- newWorkflow("wf")
w <- addJob(w, j1)
w <- addJob(w, j2)
outFile <- file.path(tempdir(), "Makefile")
writeWorkflow(w, outFile)
cat('Outputted Makefile file are in the temp directory:', outFile, '\n')