winsorize: Winsorization of copy number data

Description Usage Arguments Details Value Note Author(s) References Examples

Description

Outliers in copy number data are detected and modified using MAD or PCF Winsorization.

Usage

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winsorize(data, pos.unit = "bp", arms = NULL, method = "mad", tau = 2.5, 
          k = 25, gamma = 40, iter = 1, assembly = "hg19", digits = 4, 
          return.outliers = FALSE, save.res = FALSE, file.names = NULL, 
          verbose = TRUE)

Arguments

data

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 column(s) the numeric copy number measurements for one or more samples. The header of copy number columns should give sample IDs.

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 data. If not specified chromosome arms are found using the built-in genome assembly version determined by assembly.

method

the Winsorization method to be applied, must be one of "mad" (default) or "pcf".

tau

Winsorization threshold, default is 2.5.

k

the half window size to be applied in median filtering, default is 25.

gamma

penalty for each discontinuity in the pcf curve, default is 40. Only applicable when method="pcf".

iter

number of iterations in PCF Winsorization, default is 1.

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.outliers

logical value indicating whether a data frame identifying outliers should be returned, default is FALSE.

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 Winsorized data and outlier statuses, respectively, should be saved if save.res=TRUE.

verbose

logical value indicating whether or not to print a progress message each time Winsorization is finished for a new chromosome arm.

Details

The copy number data are either MAD Winsorized or PCF Winsorized as described in Nilsen and Liestoel et al. (2012). Winsorization is done separately on each chromosome arm in each sample.

Value

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

wins.data

a data frame with chromosome numbers in the first column, probe positions in the second and the Winsorized copy number values for the sample(s) in subsequent column(s).

wins.outliers

a data frame with chromosome numbers in the first column, probe positions in the second and outlier statuses for each sample in the subsequent column(s). The values +/- 1 indicate that the observation is an outlier, whereas the value 0 indicates that it is not.

If return.outliers = FALSE only the data frame containing the winsorized data is returned.

If save.res=TRUE the results are saved in text files with names as specified in file.names. If file.names=NULL, a folder named "Wins_res" is created in the working directory and Winsorized data and outlier statuses are saved in this directory in tab-separated files named wins.data.txt and wins.outliers.txt, respectively.

Note

Any missing values in data imply that the Winsorized value and outlier status for this probe will be missing as well. Also, if the number of probes within a chromosome arm is less than 2*k, Winsorization cannot be done and the data values are thus left unchanged.

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

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#Lymphoma data
data(lymphoma)
#Take out a smaller subset of 3 samples (using subsetData):
sub.lymphoma <- subsetData(lymphoma,sample=1:3)

#Do MAD Winsorization:
wins.data <- winsorize(data=sub.lymphoma)
         

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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 23p 
winsorize finished for chromosome arm 23q 

copynumber documentation built on May 6, 2019, 2:28 a.m.