objectsampletotemplate: Converts data of a sample in a QDNAseq-object to a template...

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

Converts data of a sample in a QDNAseq-object to a template for ACE functions

Description

objectsampletotemplate parses QDNAseq-objects into the data frame structure used by various ACE functions. These functions call objectsampletotemplate itself when necessary, but it might be convenient to make a template if you expect some repeated use of the functions or if you want to make manual adjustments to the template.

Usage

objectsampletotemplate(copyNumbersSegmented, index = 1)

Arguments

copyNumbersSegmented	QDNAseqCopyNumbers object with segmented data
index	Integer. Specifies the index of the sample

Value

Returns a template data frame with the columns bin, chromosome, copynumbers, and segments (when available)

Note

If segment values are missing, the function will still return a data frame, but only containing the copynumbers column, not the segments column

Author(s)

Jos B. Poell

See Also

singlemodel, squaremodel, singleplot

Examples

data("copyNumbersSegmented")
template <- objectsampletotemplate(copyNumbersSegmented, index = 1)

tgac-vumc/ACE documentation built on Nov. 29, 2022, 12:15 a.m.