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Last data update: 2014.03.03

R: Allele-specific copy number segmentation.

aspcf

R Documentation

Allele-specific copy number segmentation.

Description

Joint segmentation of SNP array data resulting in piecewise constant curves with common break points for copy number data and B-allelle frequency data.

Usage

aspcf(logR, BAF, pos.unit = "bp", arms = NULL, kmin = 5, gamma = 40,
      baf.thres=c(0.1,0.9), skew = 3, assembly= "hg19", digits = 4, 
      return.est = FALSE, save.res = FALSE, file.names=NULL, verbose = TRUE)

Arguments

`logR`	either a data frame or the name of a tab-separated file from which copy number data can be read. The rows of the data frame or file should represent the probes. Column 1 must hold numeric or character chromosome numbers, column 2 the numeric local probe positions, and subsequent columns the numeric copy number measurements for one or more samples. The header of copy number column(s) should give sample ID(s).
`BAF`	either a data frame or the name of a tab-separated file from which B-allelle frequency data can be read. Must be on the same format and size as `logR`, with chromosomes and local probe positions in the two first columns, and numeric BAF-measurements for one or more samples in subsequent columns.
`pos.unit`	the unit used to represent the probe positions. Allowed options are "mbp" (mega base pairs), "kbp" (kilo base pairs) or "bp" (base pairs). By default assumed to be "bp".
`arms`	optional character vector containing chromosome arms (denoted 'p' and 'q') corresponding to the chromosomes and positions found in `logR` and `BAF`. If not specified chromosome arms are found using the built-in genome assembly version determined by `assembly`.
`kmin`	minimum number of probes in each segment, default is 5.
`gamma`	penalty for each discontinuity in the curve, default is 40.
`baf.thres`	a numeric vector of length two giving the thresholds below and above which BAF probes are considered germline homozygous. Must be in the range 0 to 1, default is 0.1 and 0.9 for the lower and upper limit, respectively.
`skew`	a numeric value used to determine whether there is allelic skewness (one or two bands) in BAF. Default is 3. The larger the value the further the BAF measurements must be from 0.5 to imply two bands.
`assembly`	a string specifying which genome assembly version should be applied to determine chromosome arms. Allowed options are "hg19", "hg18", "hg17" and "hg16" (corresponding to the four latest human genome annotations in the UCSC genome browser).
`digits`	the number of decimals to be applied when reporting results. Default is 4.
`return.est`	logical value indicating whether a data frame holding LogR estimates should be returned along with the segments. Default is FALSE, which means that only segments are returned.
`save.res`	logical value indicating whether results should be saved in text files, default is FALSE.
`file.names`	optional character vector of length two giving the name of the files where the logR estimates and segments, respectively, should be saved in case `save.res=TRUE`.
`verbose`	logical value indicating whether or not to print a progress message each time aspcf analysis is finished for a new chromosome arm.

Details

Piecewise constant curves are simultaneously fitted to the LogR and BAF data as described in Nilsen and Liestoel et al.(2012). This implies that break points will be the same for the LogR and BAF segmentation curves, while segment values differ. Segmentation is done separately on each chromosome arm in each sample.

Value

If return.est = TRUE a list with the following components:

`logR_estimates`	a data frame where the first two columns give the chromosome numbers and probe positions, respectively, while subsequent column(s) give the LogR estimates for each sample. The estimate for a given probe equals the mean of the segment where the probe is located.
`segments`	a data frame describing each segment found. Each row represents a segment, and columns give the sample IDs, chromosome numbers, arms, local start positions, local end positions, number of probes in the segments, mean LogR values and mean BAF values, respectively.

If return.est = FALSE, only the data frame containing the segments is returned.

If save.res = TRUE the results are also saved in text files with names as specified in file.names. If file.names=NULL, a folder named "aspcf_results" is created in the working directory, and the LogR estimates and the segmentation results are saved in this folder as tab-separated files named logR_estimates.txt and segments.txt, respectively.

Note

It will usually be advisable to Winsorize the logR data before running aspcf, see winsorize on this. Missing values are not allowed in logR, see imputeMissing for imputation of missing copy number values.

Author(s)

Gro Nilsen, Knut Liestoel, Ole Christian Lingjaerde

References

Nilsen and Liestoel et al., "Copynumber: Efficient algorithms for single- and multi-track copy number segmentation", BMC Genomics 13:591 (2012), doi:10.1186/1471-2164-13-59

Examples

#Load LogR and BAF data:
data(logR)
data(BAF)

#First winsorize logR to handle outliers:
wins.logR <- winsorize(logR)

#Run aspcf:
aspcf.segments <- aspcf(wins.logR,BAF)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(copynumber)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/copynumber/aspcf.rd_%03d_medium.png", width=480, height=480)
> ### Name: aspcf
> ### Title: Allele-specific copy number segmentation.
> ### Aliases: aspcf
> 
> ### ** Examples
> 
> #Load LogR and BAF data:
> data(logR)
> data(BAF)
> 
> #First winsorize logR to handle outliers:
> wins.logR <- winsorize(logR)
winsorize finished for chromosome arm 1p 
winsorize finished for chromosome arm 1q 
winsorize finished for chromosome arm 2p 
winsorize finished for chromosome arm 2q 
winsorize finished for chromosome arm 3p 
winsorize finished for chromosome arm 3q 
winsorize finished for chromosome arm 4p 
winsorize finished for chromosome arm 4q 
winsorize finished for chromosome arm 5p 
winsorize finished for chromosome arm 5q 
winsorize finished for chromosome arm 6p 
winsorize finished for chromosome arm 6q 
winsorize finished for chromosome arm 7p 
winsorize finished for chromosome arm 7q 
winsorize finished for chromosome arm 8p 
winsorize finished for chromosome arm 8q 
winsorize finished for chromosome arm 9p 
winsorize finished for chromosome arm 9q 
winsorize finished for chromosome arm 10p 
winsorize finished for chromosome arm 10q 
winsorize finished for chromosome arm 11p 
winsorize finished for chromosome arm 11q 
winsorize finished for chromosome arm 12p 
winsorize finished for chromosome arm 12q 
winsorize finished for chromosome arm 13q 
winsorize finished for chromosome arm 14q 
winsorize finished for chromosome arm 15q 
winsorize finished for chromosome arm 16p 
winsorize finished for chromosome arm 16q 
winsorize finished for chromosome arm 17p 
winsorize finished for chromosome arm 17q 
winsorize finished for chromosome arm 18p 
winsorize finished for chromosome arm 18q 
winsorize finished for chromosome arm 19p 
winsorize finished for chromosome arm 19q 
winsorize finished for chromosome arm 20p 
winsorize finished for chromosome arm 20q 
winsorize finished for chromosome arm 21q 
winsorize finished for chromosome arm 22q 
winsorize finished for chromosome arm Xp 
winsorize finished for chromosome arm Xq 
> 
> #Run aspcf:
> aspcf.segments <- aspcf(wins.logR,BAF)
aspcf finished for chromosome arm 1p 
aspcf finished for chromosome arm 1q 
aspcf finished for chromosome arm 2p 
aspcf finished for chromosome arm 2q 
aspcf finished for chromosome arm 3p 
aspcf finished for chromosome arm 3q 
aspcf finished for chromosome arm 4p 
aspcf finished for chromosome arm 4q 
aspcf finished for chromosome arm 5p 
aspcf finished for chromosome arm 5q 
aspcf finished for chromosome arm 6p 
aspcf finished for chromosome arm 6q 
aspcf finished for chromosome arm 7p 
aspcf finished for chromosome arm 7q 
aspcf finished for chromosome arm 8p 
aspcf finished for chromosome arm 8q 
aspcf finished for chromosome arm 9p 
aspcf finished for chromosome arm 9q 
aspcf finished for chromosome arm 10p 
aspcf finished for chromosome arm 10q 
aspcf finished for chromosome arm 11p 
aspcf finished for chromosome arm 11q 
aspcf finished for chromosome arm 12p 
aspcf finished for chromosome arm 12q 
aspcf finished for chromosome arm 13q 
aspcf finished for chromosome arm 14q 
aspcf finished for chromosome arm 15q 
aspcf finished for chromosome arm 16p 
aspcf finished for chromosome arm 16q 
aspcf finished for chromosome arm 17p 
aspcf finished for chromosome arm 17q 
aspcf finished for chromosome arm 18p 
aspcf finished for chromosome arm 18q 
aspcf finished for chromosome arm 19p 
aspcf finished for chromosome arm 19q 
aspcf finished for chromosome arm 20p 
aspcf finished for chromosome arm 20q 
aspcf finished for chromosome arm 21q 
aspcf finished for chromosome arm 22q 
aspcf finished for chromosome arm Xp 
aspcf finished for chromosome arm Xq 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>