Description Usage Arguments Details Value Examples
Makes methylation count matrix using output from either BSMAP or Bismark.
1 | getmethmat(filnames, sample.id, filtype = "bsmap")
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filnames |
input filenames |
sample.id |
sample IDs |
filtype |
"bsmap", "bismarkCoverage","bismarkCytosineReport". Default is "bsmap". "bismarkCoverage" files, have the columns: chr,start,end, number of cytosines (methylated bases) and number of thymines (unmethylated bases). "bismarkCytosineReport" have the columns: chr,start, strand, number of cytosines (methylated bases) , number of thymines (unmethylated bases),context and trinucletide context format. |
Removes sites with 0 counts in all samples.
Input file from BSMAP has columns: chromosome, position, strand, context, ratio, eff_CT_count, C_count, CT_count, rev_G_count, rev_GA_count, CI_lower, CI_upper.
Input file from Bismark coverage for CG only has columns "chrBase","chr","base","strand","coverage","freqC","freqT"
Sample input files from BSMAP: sample1_methratio.txt, sample1_mehtratio.txt
For BSMAP input files, extracts CpGs and output in filname.CpG in the current working directory. Adds "Chr" to chromosome name and output in filname.CpG_chr.
methylation count matrix where rows are CpG sites and columns are: chromosome, start, end, strand, number of Ts+Cs for sample 1, number of Cs for sample 1, number of Ts for sample 1, ....
1 2 3 4 5 6 | ## Not run:
file1 = system.file("extdata","sample1_methratio.txt", package="deconvSeq")
file2 = system.file("extdata","sample2_methratio.txt", package="deconvSeq")
methmat = getmethmat(filnames=c(file1,file2), sample.id=c("sample1","sample2"), filtype="bsmap")
## End(Not run)
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