slice1 {TransView} | R Documentation

## 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

    ## S4 method for signature 'DensityContainer,character,numeric,numeric'
    slice1(dc, chrom, start, end, control=FALSE, input_method="-",treads_norm=TRUE, nbins=0, bin_method="mean")
    ## S4 method for signature 'DensityContainer'
    sliceN(dc, ranges, toRle=FALSE, control=FALSE, input_method="-",treads_norm=TRUE, nbins=0, bin_method="mean")

### Arguments

`dc` | 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’.

### 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.

### Value

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

### Author(s)

Julius Muller ju-mu@alumni.ethz.ch

### See Also

- `slice1T`.

- DensityContainer-class.

### Examples

    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))

[Package TransView version 1.28.0 Index]