filterLoci {biscuiteer} | R Documentation |
Function potentially used to be a part of dmrseq. Included here to avoid dmrseq failing due to any number of reasons related to lack of coverage.
filterLoci(bsseq, testCovariate)
bsseq |
A bsseq object for filtering |
testCovariate |
The name of the pData column dmrseq will test on |
The code is adapted from the precheck loop of dmrseq::dmrseq
A bsseq object ready for dmrseq to use
dmrseq
WGBSeq
RRBSeq
shuf_bed <- system.file("extdata", "MCF7_Cunha_chr11p15_shuffled.bed.gz", package="biscuiteer") orig_bed <- system.file("extdata", "MCF7_Cunha_chr11p15.bed.gz", package="biscuiteer") shuf_vcf <- system.file("extdata", "MCF7_Cunha_shuffled_header_only.vcf.gz", package="biscuiteer") orig_vcf <- system.file("extdata", "MCF7_Cunha_header_only.vcf.gz", package="biscuiteer") bisc1 <- readBiscuit(BEDfile = shuf_bed, VCFfile = shuf_vcf, merged = FALSE) bisc2 <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf, merged = FALSE) comb <- unionize(bisc1, bisc2) filt <- filterLoci(comb, "sampleNames")