CNprep (version 2.0)

makeCNPmask: Given a set of copy-number events, create a DNA copy-number mask

Description

The function takes as an input a set of intervals with integer-valued boundary positions. It then finds interval regions where the event count is above each of two thresholds, upper and lower, and returns those interval regions with the count above the lower threshold that contain interval regions with the count above the upper threshold.

Usage

makeCNPmask(imat,chromcol=1,startcol=2,endcol=3,nprof=1,uthresh,dthresh)

Arguments

imat

A matrix or a data frame tabulating the chromosome number and endpoint positions of the interval events.

chromcol,startcol, endcol

Character strings or integers specifying the columns of imat containing the chromosome number and the left (right) endpoint positions of the interval events.

nprof

An integer specifying the number of copy number profiles from which the events originate.

uthresh, dthresh

Numeric, specifying the upper and lower thresholds for the event frequency or (if nprof =1) for the event count.

Value

An integer matrix with three columns, called "chrom","start" and "end", specifying the chromosome number and boundary positions of the mask.

Examples

# NOT RUN {
#load a table of copy number events collected from 1203 profiles.
data(cnpexample)
#Create a table of gain (amplification) events only.
amps<-cnpexample[cnpexample[,"copy.num"]=="amp",]
#Create a mask using this table.
ampCNPmask<-makeCNPmask(imat=amps,chromcol="chrom",startcol="chrom.start",
endcol="chrom.end",nprof=1203,uthresh=0.02,dthresh=0.008)
# }