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

In genomation: Summary, annotation and visualization of genomic data

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)

## S4 method for signature '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)

genomation documentation built on Nov. 8, 2020, 5:21 p.m.