genomation (version 1.4.2)

intersectScoreMatrixList: Get common rows from all matrices in a ScoreMatrixList object

Description

Returns a intersection of rows for each matrix in a ScoreMatrixList object. This is done using the rownames of each element in the list.

Usage

intersectScoreMatrixList(sml, reorder = FALSE)
## S3 method for class 'ScoreMatrixList':
intersectScoreMatrixList(sml, reorder = FALSE)

Arguments

sml

a ScoreMatrixList object

reorder

if TRUE ScoreMatrix objects in the list are sorted based on their common row ids.

Value

• ScoreMatrixList object

Examples

library(GenomicRanges)
target = GRanges(rep(c(1,2),each=7),
                  IRanges(rep(c(1,1,2,3,7,8,9), times=2), width=5),
                  weight = rep(c(1,2),each=7))

windows1 = GRanges(rep(c(1,2),each=2),
                    IRanges(rep(c(1,2), times=2), width=5),
                    strand=c('-','+','-','+'))
windows2 = windows1[c(1,3)]
sml = as(list(ScoreMatrix(target, windows1),
               ScoreMatrix(target, windows2)), 'ScoreMatrixList')
sml
intersectScoreMatrixList(sml)