validateMakeCNPmask: Parameters validation for the 'makeCNPmask' function

In KrasnitzLab/CNprep: Pre-process DNA Copy Number (CN) Data for Detection of CN Events

Parameters validation for the makeCNPmask function

Description

Validation of all parameters needed by the public makeCNPmask function.

Usage

validateMakeCNPmask(imat, chromCol, startCol, endCol, nProf, uThresh, dThresh)

Arguments

imat	A matrix or a data.frame tabulating the chromosome numbers and startpoint/endpoint positions of the interval events.
chromCol	A character string or numeric representing an integer specifying the column of imat containing the chromosome numbers of the interval events.
startCol	A character string or numeric representing an integer specifying the column of imat containing the left (right) endpoint of the interval events.
endCol	A character string or numeric representing an integer specifying the column of imat containing the right endpoint of the interval events.
nProf	A positive numeric acting as an integer specifying the number of copy number profiles from which the events originated.
uThresh	A numeric specifying the upper ratio threshold for the event frequency or (if nProf = 1) for the event count. The upper ratio threshold must be equal or superior to the lower threshold (dThresh). The upper ratio threshold must also be between 0 and 1.
dThresh	A numeric specifying the lower ratio threshold for the event frequency or (if nProf = 1) for the event count. The lower ratio threshold must be equal or inferior to the upper threshold (dThresh). The lower ratio threshold must also be between 0 and 1.

Value

0.

Author(s)

Astrid Deschênes

Examples

data(segexample)

## Return zero as all parameters are valid
CNprep:::makeCNPmask(imat=segexample, chromCol="chrom",
    startCol="start", endCol="end", nProf=1203, uThresh=0.20, dThresh=0.10)

KrasnitzLab/CNprep documentation built on May 28, 2022, 8:32 p.m.