| Type: | Package |
| Title: | Annotate the Gene Symbols for Probes in Expression Array |
| Version: | 0.1.7 |
| Date: | 2022-11-12 |
| Maintainer: | Yonghe Xia <xiayh17@gmail.com> |
| Description: | We curated 147 of expression array, from 3 species(human,mouse,rat), 3 companies('Affymetrix','Illumina','Agilent'), by aligning the 'Fasta' sequences of all probes of each platform to their corresponding reference genome, and then annotate them to genes. |
| License: | Apache License (≥ 2) |
| Encoding: | UTF-8 |
| URL: | https://github.com/jmzeng1314/AnnoProbe |
| LazyData: | true |
| RoxygenNote: | 7.1.1 |
| Depends: | R (≥ 3.4.0) |
| Imports: | ggplot2, DT, ggpubr, pheatmap, utils, methods, Biobase, stats, xml2, httr, curl |
| biocViews: | DataImport, Microarray, OneChannel, SAGE, Software, TwoChannel |
| Suggests: | limma, GEOquery, knitr, rmarkdown |
| NeedsCompilation: | no |
| Packaged: | 2022-11-12 11:39:35 UTC; xiayh |
| Author: | Jianming Zeng [aut], Yujia Xiang [aut], Yonghe Xia [ctb, cre] |
| Repository: | CRAN |
| Date/Publication: | 2022-11-14 08:30:11 UTC |
An example dataset
Description
A dataset containing genes_expr, group_list, DEG
Usage
GSE27533
Format
A list with 6 elements:
- genes_expr
genes_expr, genes_expr
- DEG
DEG, DEG
...
An example dataset
Description
A dataset containing eSet, probes_expr, probe2gene, genes_expr, group_list, DEG
Usage
GSE95166
Format
A list with 6 elements:
- probes_expr
probes_expr, probes_expr
- probe2gene
probe2gene, probe2gene
- genes_expr
genes_expr, genes_expr
- group_list
group_list, group_list
- DEG
DEG, DEG
...
Annotate gene IDs according to GTF files in gencode
Description
annoGene will return a data.frame of gene information or write them to a file (csv or html format). The user should set a list of genes to be annotated, with "ENSEMBL" or "SYMBOL" style.
Usage
annoGene(IDs, ID_type, species = "human", out_file)
Arguments
IDs |
a list of genes |
ID_type |
the type of input IDs, should be "ENSEMBL" or "SYMBOL" |
species |
choose human or mouse, or rat, default: human |
out_file |
the filename, should be ".csv" or ".html". |
Value
a dataframe which columns contain genesymbol, biotypes, ensembl ids and the positions of genes
Examples
IDs <- c("DDX11L1", "MIR6859-1", "OR4G4P", "OR4F5")
ID_type = "SYMBOL"
annoGene(IDs, ID_type)
annoGene(IDs, ID_type,out_file = tempfile(fileext = ".html"))
annoGene(IDs, ID_type,out_file = tempfile(fileext = ".csv"))
Check whether the input gpl in our platform list or not
Description
Check whether the input gpl in our platform list or not
Usage
checkGPL(GPL = NULL)
Arguments
GPL |
GPL(GEO platform) number, eg: GPL570 |
Value
returns a boolean value
Examples
checkGPL('GPL570')
checkGPL('GPL15314')
checkGPL('GPL10558')
Check a list of genes how they show difference.
Description
How does a gene or a list of genes show difference between two group. The boxplot or heatmap will be drawed. just a wrap function of ggpubr and pheatmap.
Usage
check_diff_genes(gene, genes_expr, group_list)
Arguments
gene |
A vector contains all gene ids of interest. Gene ids should be gene symbol. |
genes_expr |
An expression matrix, the rownames should be gene symbol. |
group_list |
A vector contains the group information of each samples in expression matrix |
Value
A figure : boxplot or heatmap
Examples
attach(GSE95166)
check_diff_genes('LRCH3',genes_expr,group_list )
x=DEG$logFC
names(x)=rownames(DEG)
cg=c(names(head(sort(x),100)), names(tail(sort(x),100)))
check_diff_genes(cg,genes_expr,group_list )
draw a heatmap for DEG result
Description
deg_heatmap will draw a heatmap for you.
Usage
deg_heatmap(deg, genes_expr, group_list, topn = 20)
Arguments
deg |
the result from limma. |
genes_expr |
the expression matrix |
group_list |
a vector |
topn |
the number of genes in heatmap, default:20 |
Value
a ggplot2 style figure.
Examples
attach(GSE27533)
deg_heatmap(DEG,genes_expr,group_list)
draw a volcano for DEG result
Description
deg_volcano will draw a volcano for you.
Usage
deg_volcano(need_deg, style = 1, p_thred = 0.05, logFC_thred = 1)
Arguments
need_deg |
should be 3 columns : gene, logFC, p.value(or p.adjust |
style |
you can try 1 or 2, default: 1 |
p_thred |
default:0.05 |
logFC_thred |
default:1 |
Value
a ggplot2 style figure.
Examples
deg=GSE27533$DEG
need_deg=data.frame(symbols=rownames(deg), logFC=deg$logFC, p=deg$P.Value)
deg_volcano(need_deg,2)
deg_volcano(need_deg,1)
Filter expression matrix based on annotation
Description
filterEM will annotate the probes in expression matrix and remove the duplicated gene symbols.
because there will be many probes mapped to same genes, we will only keep the max value one.
Usage
filterEM(probes_expr, probe2gene)
Arguments
probes_expr |
is an expression matrix which rownames are probes of probe2gene and each column is a sample |
probe2gene |
the first column is probes and the second column is corresponding gene symbols |
Value
a expression matrix which has been filtered duplicated gene symbols
Examples
attach(GSE95166)
# head(probes_expr)
# head(probe2gene)
genes_expr <- filterEM(probes_expr,probe2gene)
# head(genes_expr)
Download expression dataset by GSE id
Description
geoChina will download the expression matrix and phenotype data as ExpressionSet format
from cloud in mainland China,
it's a alternative method for getGEO function from GEOquery package.
geoChina('gse1009') is the same as eSet=getGEO('gse1009', getGPL = F)
Usage
geoChina(gse = "GSE2546", mirror = "tencent", destdir = getwd())
Arguments
gse |
input GSE id, such as GSE1009, GSE2546, gse1009. |
mirror |
"tencent" only for now. |
destdir |
The destination directory for data downloads. |
Value
a list of ExpressionSet, which contains the expression matrix and phenotype data
Examples
## Not run:
geoChina('GSE1009',destdir=tempdir())
## End(Not run)
Get all GPL list in our package
getGPLList returns all the GPL number checklist stored in package
Description
Get all GPL list in our package
getGPLList returns all the GPL number checklist stored in package
Usage
getGPLList()
Value
a data.frame which contains the gpl and name of array.
Get Probe Annotation
Description
idmap returns probe annotations for input gpl
Usage
idmap(gpl = "GPL570", type = "bioc", mirror = "tencent", destdir = getwd())
Arguments
gpl |
GPL(GEO platform) number, eg: GPL570 |
type |
source of probe anntation stored, one of "pipe", "bioc", "soft", default:"pipe" |
mirror |
"tencent" only for now |
destdir |
The destination directory for data downloads. |
Value
probe annotaions
Examples
ids=idmap('GPL570',destdir=tempdir())
ids=idmap('GPL570',type='soft',destdir=tempdir())
ids=idmap('GPL18084',type='pipe',destdir=tempdir())
Print GPL information
Description
Print GPL information
Usage
printGPLInfo(GPL = NULL)
Arguments
GPL |
GPL(GEO platform) number, eg: GPL570 |
Value
print detail information of the input GEO platform
Examples
printGPLInfo('GPL93')