meltPeak: Convenience function which returns a data frame with...

In TransView: Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Description

Returns a data frame with labels and normalized densities of the provided DensityContainer

Usage

meltPeak(..., region, control=FALSE, peak_windows = 0, bin_method="mean", rpm=TRUE, smooth=0)

Arguments

...	DensityContainer objects
region	Can be one entry of the annotated output of annotatePeaks or a GRanges object with one entry and with a transcript_id and distance metadata column.
control	An optional vector of DensityContainer objects, that have to match the order of experiments passed as a first argument. E.g. plotTV(ex1.ChIP,ex2.ChIP,control=c(ex1.Input,ex2.Input). The content will be treated as background densities and subtracted from the matching experiment.
peak_windows	If set to an integer greater than 0, all binding profiles will be interpolated into this amount of windows by the method specified by bin_method.
bin_method	Specifies the function used to summarize the bins specified by nbins. Possible methods are ‘max’, ‘mean’, ‘median’ or ‘approx’ for linear interpolation.
rpm	If set to TRUE, all sample groups will be normalized to Reads Per Million mapped reads after quality filtering according to the filtered_reads slot of the DensityContainer. Should not be set in truncated density maps!
smooth	If greater than 0, smooth defines the smoother span as described in the function lowess. This function will be applied to reads or RPM values, depending on rpm and the results will be stored in the column ‘Smooth’.

Details

Convenience function which returns a data frame with one row per BP or, if peak_window greater than zero, per peak_window. The label will be taken from the ex_name slot of the DensityContainer. The slot should be set to meaningful names before using this function. All read densities will be normalized to the total map mass and if a control is provided also background subtracted.

Value

data.frame with 3 columns: ‘NormalizedReads’, ‘Label’ and ‘Position’. Optionally a column ‘Smooth’ will be appended.

Author(s)

Julius Muller [e-mail]

Examples

exbam<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="bam$")
exls<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="xls$")
exgtf<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="gtf.gz$")[2]
fn.macs<-dir(system.file("extdata", package="TransView"),full=TRUE,patt="xls$")

exden.ctrl<-parseReads(exbam[1],verbose=0)
exden.chip<-parseReads(exbam[2],verbose=0)

peaks<-macs2gr(exls,psize=500)

GTF<-gtf2gr(exgtf)
peaks<-macs2gr(fn.macs,psize=500)
peaks.anno<-annotatePeaks(peaks=peaks,gtf=GTF)

peak1.df<-meltPeak(exden.chip,region=peaks.anno["Peak.1"],bin_method="mean",peak_windows=100,rpm=TRUE)
head(peak1.df)

TransView documentation built on Nov. 8, 2020, 5:31 p.m.