readMeths {segmentSeq} | R Documentation |
This function takes as input a set of files that describe the number of
times a set of cytosines are observed to be methylated or unmethylated
in some high-throughput sequencing data. It merges the data from these
files into an object of 'alignmentMeth
' class which can
then be further processed to identify methylation loci.
readMeths(files, dir = ".", libnames, replicates, nonconversion, chrs)
files |
A character vector defining the file names of the alignment files to be read in. |
dir |
The directory in which the files are located. |
libnames |
A character vector giving the names of the samples to be read in. |
replicates |
A vector defining the replicate structure of the data. The ‘i’th and ‘j’th libraries are treated as replicates if and only if replicates[i] == replicates[j]. |
nonconversion |
A numeric vector (all members should lie between 0 and 1) defining the
non-conversion rate of each library. See
|
chrs |
An (optional) character vector giving the names of the chromosomes to be read from the files. If ommitted, all chromosomes will be read in. |
An object of class alignmentMeth
.
Thomas J. Hardcastle
datadir <- system.file("extdata", package = "segmentSeq") files <- c("short_18B_C24_C24_trim.fastq_CG_methCalls.gz", "short_Sample_17A_trimmed.fastq_CG_methCalls.gz", "short_13_C24_col_trim.fastq_CG_methCalls.gz", "short_Sample_28_trimmed.fastq_CG_methCalls.gz") mD <- readMeths(files = files, dir = datadir, libnames = c("A1", "A2", "B1", "B2"), replicates = c("A","A","B","B"), nonconversion = c(0.004777, 0.005903, 0.016514, 0.006134))