forcesegmentsontemplate: Custom resegmentation with user-defined segment information

In ACE: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Description

forcesegmentsontemplate forces a user-defined segmentation pattern on a template. The input containing the segment information requires the chromosome name, start position, and end position of the segments. This can be provided manually as a data frame or as a data frame such as obtained by getadjustedsegments. This means you can also use this function to force the segment pattern of one sample onto another sample. It is possible to retain the break points of the original input template.

Usage

forcesegmentsontemplate(segmentinput, template, QDNAseqobjectsample = FALSE, 
                        combinesegments = FALSE, funtype = 'mean')

Arguments

segmentinput	Data frame containing segment information. Requires columns with chromosome name, start position, and end position. The function looks for column names containing "chr", "start", and "end" to find the required information
template	Object. Either a data frame as created by objectsampletotemplate, or a QDNAseq-object. Note that segmented data is not required for this function, unless combining segments
QDNAseqobjectsample	Integer. Specifies which sample to use as input from the QDNAseq-object. Required when using a QDNAseq-object as template. Default = FALSE
combinesegments	Logical. When TRUE, segment break points from the input template are retained. Default = FALSE
funtype	Character string. Specifies which function to use to calculate segment values. An alternative would be 'median'. Default = 'mean'

Details

This function only changes (or adds) the segments column of the input template. Copynumbers values are always retained, even if they fall out of the range of the segmentinput.

Value

Returns a template data frame with the columns bin, chromosome, copynumbers, and segments

Author(s)

Jos B. Poell

See Also

getadjustedsegments, twosamplecompare

Examples

data("copyNumbersSegmented")
template <- objectsampletotemplate(copyNumbersSegmented, index = 1)
segments <- getadjustedsegments(copyNumbersSegmented, 2)[,1:3]
newtemplate <- forcesegmentsontemplate(segments, template)
first50M <- forcesegmentsontemplate(data.frame(chr = 1:22, 
  start = rep(1, 22), end = rep(50000000, 22)), template)
singleplot(first50M)

ACE documentation built on Nov. 8, 2020, 5:30 p.m.