Discriminating Probes Selection

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Documentation for package ‘disprose’ version 0.1.6

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add_adapters Add adapters to probes
ann.data Chlamydia pneumoniae genome annotation.
annotate_probes Annotate probes
blast.fill Local BLAST results with added content.
blast.raw Local BLAST results.
blast_local Local BLAST
count_GC Calculate physical and chemical properties
count_MFE Calculate physical and chemical properties
count_PhCh Calculate physical and chemical properties
count_REP Calculate physical and chemical properties
count_TM Calculate physical and chemical properties
cut_probes Cut probes
cut_string Cut string into segments
delete_AcNum_version Complement BLAST result
delete_duplicates_DF Delete rows with duplicated values
delete_from_DB Store data in SQLite database
fill_blast_result Complement BLAST result
fill_blast_results Complement BLAST result
get_GA_files Read GISAID sequence file
get_GIs Get GenInfo Identifier numbers
get_GIs_fix Get GenInfo Identifier numbers
get_seq_for_DB Get nucleotide sequences from NCBI
get_seq_for_DB_fix Get nucleotide sequences from NCBI
get_seq_info Get NCBI sequence record
get_seq_info_fix Get NCBI sequence record
index_DB Store data in SQLite database
info_listtodata Get NCBI sequence record
list_DB Store data in SQLite database
make_blast_DB Builds local database for BLAST
make_ids Create unique identification values
meta.all Metadata of all available Chlamydia pneumoniae's sequences.
meta.target Metadata of target Chlamydia pneumoniae's sequences.
normalize_DF Normalize variable
rate_DF Rate variables
read_and_unite_files Read and unite files
read_from_DB Store data in SQLite database
read_from_table_file Read table file
store_in_DB Store data in SQLite database
summarize_blast_result Summarize BLAST result
trim_DF Trim data frame
unite_NCBI_ac.nums Assigns master record's id to all project records
unite_two_DF Combine two data frames
write_to_DB Store data in SQLite database