slice1: Slice read densities from a TransView dataset

Description

slice1 returns read densities of a genomic interval. sliceN takes a GRanges object or a data.frame with genomic coordinates and returns a list of read densities.

Usage

"slice1"(dc, chrom, start, end, control=FALSE, input_method="-",treads_norm=TRUE, nbins=0, bin_method="mean")
"sliceN"(dc, ranges, toRle=FALSE, control=FALSE, input_method="-",treads_norm=TRUE, nbins=0, bin_method="mean")

Arguments

Source DensityContainer object

chrom

A case sensitive string of the chromosome

start,end

Genomic start and end of the slice

ranges

A GRanges object or a data.frame.

toRle

The return values will be converted to a RleList.

control

An optional DensityContainer which will used as control and by default subtracted from dc.

input_method

Defines the handling of the optional control DensityContainer. ‘-’ will subtract the control from the actual data and ‘/’ will return log2 fold change ratios with an added pseudo count of 1 read.

treads_norm

If TRUE, the input densities are normalized to the read counts of the data set. Should not be used if one of the DensityContainer objects does not contain the whole amount of reads by e.g. placing a filter in parseReads.

nbins

If all input regions have equal length and nbins greater than 0, all densities will be summarized using the method specified by bin_method into nbins windows of approximately equal size.

bin_method

Character string that specifies the function used to summarize or expand the bins specified by nbins. Valid methods are ‘max’, ‘mean’ or ‘median’.

Value

slice1 returns a numeric vector of read densities sliceN returns a list of read densities and optionally an RleList

Details

slice1 is a fast method to slice a vector of read densities from a DensityContainer object. The vector can be optionally background subtracted. If the query region exceeds chromosome boundaries or if an non matching chromosome name will be passed, a warning will be issued and a NULL vector will be returned.

sliceN returns a list with N regions corresponding to N rows in the GRanges object or the data.frame. A list with the corresponding read densities will be returned and row names will be conserved. Optionally the return values can be converted to a RleList for seamless integration into the IRanges package.

Examples

Run this code


exbam<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="bam$")
exls<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="xls$")

#store density maps of the whole sam/bam file in test_data
exden.ctrl<-parseReads(exbam[1],verbose=0)
exden.chip<-parseReads(exbam[2],verbose=0)

peaks<-macs2gr(exls,psize=500)

#returns vector of read counts per base pair
slice1(exden.chip,"chr2",30663080,30663580)[300:310]
slice1(exden.ctrl,"chr2",30663080,30663580)[300:310]
slice1(exden.chip,"chr2",30663080,30663580,control=exden.ctrl,treads_norm=FALSE)[300:310]

xout<-sliceN(exden.chip,ranges=peaks)
lapply(xout,function(x)sum(x)/length(x))
xout<-sliceN(exden.ctrl,ranges=peaks)
lapply(xout,function(x)sum(x)/length(x))
xout<-sliceN(exden.chip,ranges=peaks,control=exden.ctrl,treads_norm=FALSE)
lapply(xout,function(x)sum(x)/length(x))