import-bcf {AllelicImbalance} | R Documentation |
Imports a selection of a bcf file or files specified by a GenomicRanges object as search area.
impBcfGRL(UserDir, ...) ## S4 method for signature 'character' impBcfGRL(UserDir, searchArea = NULL, verbose = TRUE, ...) impBcfGR(UserDir, ...) ## S4 method for signature 'character' impBcfGR(UserDir, searchArea = NULL, verbose = TRUE, ...)
UserDir |
The relative or full path of folder containing bam files. |
... |
parameters to pass on |
searchArea |
A |
verbose |
Setting |
A wrapper to import bcf files into R in the form of GenomicRanges objects.
BcfImpGRList
returns a GRangesList object. BcfImpGR
returns one GRanges object of all unique entries from one or more bcf files.
Make sure there is a complementary index file *.bcf.bci
for
each bcf file in UserDir
. If there is not, then the functions
impBcfGRL
and impBcfGR
will try to create them.
Jesper R. Gadin, Lasse Folkersen
The impBamGRL for importing bam files
The getAlleleCounts
for how to get allele(SNP) counts
The scanForHeterozygotes
for how to find possible
heterozygote positions
#Declare searchArea searchArea <- GRanges(seqnames=c('17'), ranges=IRanges(79478301,79478361)) #Relative or full path pathToFiles <- system.file('extdata/ERP000101_subset', package='AllelicImbalance') #import reads <- impBcfGRL(pathToFiles, searchArea, verbose=FALSE)