run.absCNSeq: main function to run absCNseq

Description Usage Arguments Details Value Author(s) Examples

View source: R/absCNSeq.R

Description

This wrapper function accepts data files and user specified parameters and runs the absCNseq algorithm (modify input interface from absCNseq V1.0).

Usage

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run.absCNSeq(seg.data, snv.data = NULL, res.dir, smp.name, seq.type = c("WES", "WGS"), alpha.min = 0.2, alpha.max = 1, tau.min = 1.5, tau.max = 5, min.freq = 0, min.seg.len = 0, qmax = 7, lamda = 0.5, verbose = FALSE)

Arguments

seg.data

A data frame of 5 cols with colnames being chrom,loc.start,loc.end,eff.seg.len,normalized.ratio.

snv.data

A data frame of 3 cols with colnames being chrom,position,tumor_var_freq.

res.dir

The output directory

smp.name

Sample name

seq.type

Either "WES" (whole exome sequencing) or "WGS" (whole genome sequencing)

alpha.min

The minimum allowed value for tumor purity. Default is 0.20. If you do have the pathologist estimate, set it as the lower bound of the pathologist estimate is usually preferred.

alpha.max

The maximum allowed value for tumor purity. Default is 1.0. If you do have the pathologist estimate, set it as the upper bound of the pathologist estimate is usually preferred.

tau.min

The minimum allowed value for tumor ploidy

tau.max

The maximum allowed value for tumor ploidy

min.sol.freq

A solution should appear at least this many times to be kept. Singleton solutions are usually not trustable. By default (min.sol.freq=0), the program will only retain solutions that cover at least 1 percent of the search space.

min.seg.len

The minimum length of a segment to be included in computation. The default value is 200 bp for WES and 3000 bp for WGS.

qmax

Maximum allowed absolute copy number for any segments.

lamda

The relative weight of the segment copy ratio data over the SNV data. Must be a value in(0.0,1.0].

verbose

Details

Please refer to the "example" folder to see the format of the input segmentation file or SNV file.

Value

a list is returned

searchRes

a data frame giving the solution set (purity and ploidy pairs) ranked by their fitting errors

absCN

a data frame giving the absolute copy number estimates of tumor cells for the top first solution (purity and ploidy pair)

absSNV

a data frame giving the absolute multiplicity estimates of SNVs for the top first solution (purity and ploidy pair)

orig.seg.dat

original copy ratio data read from the input segmentation file

seg.dat

filtered copy ratio data

orig.snv.dat

original SNV data read from the input SNV file

snv.dat

filtered SNV data

Author(s)

Lei Bao

Examples

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data("absCNseq", package="lxctk")
my.res.list <- run.absCNSeq(cn, snv, "myResult", "Sample1", seq.type="WES", min.seg.len=200)
seg.CN <- compute.absCN(my.res.list$seg.dat, my.res.list$searchRes[i,"alpha"], my.res.list$searchRes[i,"tau"])  # the i-th solution
plot.absCN(seg.CN, chromnum=1)  # plot chromosome 1

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.