CINdex (version 1.0.2)

run.cin.cyto: Calculate cytoband CIN

Description

run.cyto.chr calculates cytoband level CIN for the following default thresholds (with and without normalization): (a) gain threshold 2.5 and loss threshold 1.5 (b) gain threshold 2.25 and loss threshold 1.75 (c) gain threshold 2.10 and loss threshold 1.90. For each of these threshold settings, this function will calculate CIN for gains, losses, and a combination of gains and losses (referred to as 'sum' or 'overall' CIN). This will allow user to examine and select the best setting of gain and loss threshold for their data. More details and tutorial are given in the accompanying vignette.

Usage

run.cin.cyto(grl.seg, cnvgr = NULL, snpgr = NULL, genome.ucsc, out.folder.name = "output_cyto_cin", thr.gain = c(2.5, 2.25, 2.1), thr.loss = c(1.5, 1.75, 1.9), V.def = 2:3, V.mode = c("sum", "amp", "del"), chr.num = 22)

Arguments

grl.seg

The result of any segmentation algorithm such as CBS,FMR. Should be a GRangesList

cnvgr

Probe annotation info for the copy number probes - GRanges object

snpgr

Probe annotation info for the SNP probes - GRanges object

genome.ucsc

A Reference genome

out.folder.name

Name of output folder, where the CIN objects for each setting will be created

thr.gain

A numeric list that contains values set as threshold gain

thr.loss

A numeric list that contains values set as threshold loss

V.def

An integer vector that has 2 different CIN definitions - normalized (value=2) and un-normalized (value=3)

V.mode

A vector that has 3 options: 'sum', 'amp' and 'del'

chr.num

Number of chromosomes in input. Typically 22.

Value

Creates a dataMatrix and cytobands.cin R objects for each setting that contains CIN values

See Also

Accompanying vignette for complete end-to-end tutorial

Examples

#### For this example, we run cytoband CIN calculation for one setting on chromosome 1 only
data("grl.data") #need segment level data

#getting genome reference file
data("hg18.ucsctrack")
hg18.ucsctrack.chr <- subset(hg18.ucsctrack, seqnames(hg18.ucsctrack) %in% "chr22")

#get probe annotation information
data("cnvgr.18.auto")

#Call function to run cytoband CIN
run.cin.cyto(grl.seg = grl.data, cnvgr=cnvgr.18.auto, snpgr=NULL,
genome.ucsc = hg18.ucsctrack.chr, thr.gain = 2.25,thr.loss = 1.75,
V.def = 3, V.mode="sum",chr.num = 22)

#Run cytoband level CIN calculation for all thresholds. This is how command should be run:
## Not run: 
# run.cin.cyto(grl.seg = grl.data, cnvgr=cnvgr.18.auto, snpgr=snpgr.18.auto,
# genome.ucsc = hg18.ucsctrack)
# ## End(Not run)
# A number of RData objects will be created in 'output_cyto' folder.