getcounts: Make a count matrix
In lamortenera/epicseg: Chromatin Segmentation in R

Description Usage Arguments Value

Make a count matrix from a GRanges object and a list of bam files

1 2	getcounts(regions, bamtab, binsize = 200, repFun = defaultRepFun, nthreads = 1)

`regions`	GRanges object containing the genomic regions of interest. Each region will be divided into non-overlapping bins of equal size. The reads falling in each bin will be the elements of the final count matrix.
`bamtab`	Data frame describing how to get the counts from each file. The following columns are required: 'mark' (name of the histone mark), 'path' (path to the bam file). The following columns are optional: 'mapq' (minimum mapping quality), 'shift' (shift in the 3' to 5' direction applied to each read), 'pairedend' (paired end mode or not)
`binsize`	The size of each bin in basepairs. Each region must have a width multiple of `binsize`, otherwise an error will be thrown. Use the function `refineRegions` to make sure that your GRanges object satisfies this constraint.
`repFun`	In case there are replicate experiments (i.e. entries in bampath with the same 'mark' name), they will be collapsed into one experiment using this function. This function takes a matrix of counts as input where the columns are different experiments and the rows are different bins and returns a vector with as many elements as the rows of the input matrix.
`nthreads`	Number of threads. Parallelization is done on the histone marks using `mclapply`.

A count matrix where the rows are the different marks labelled with the names of the list marks, and the columns are the different bins in the regions.

lamortenera/epicseg documentation built on May 20, 2019, 7:34 p.m.