selectSegments: Select multipcf segments

In copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression.

Description

Selects multipcf segments based on a desired characteristic.

Usage

 selectSegments(segments, what = "variance", thres = NULL, nseg = 10, 
                  large = TRUE, p = 0.1)

Arguments

segments	a data frame containing segments found by multipcf.
what	the desired characteristic to base selection on. Must be one of "variance" (default),"length" and "aberration". See details below.
thres	an optional numeric threshold to be applied in the selection.
nseg	the desired number of segments to be selected, default is 10. Only used if thres=NULL.
large	logical value indicating whether segments with large (TRUE) or small (FALSE) variance, length or mean value should be selected when what is "variance", "length" or "aberration", respectively.
p	a number between 0 and 1 giving the minimum proportion of samples for which an aberration must be detected, default is 0.1. Only applicable if what="aberration".

Details

The input in what determines how the segments are selected. Three options are available:

If what="variance" the variance of the segment values across all samples is calculated for each segment. If thres is specified, the subset of segments for which the variance is above (if large=TRUE) or below (if large=FALSE) the threshold is returned. If thres is not given by the user, a given number of segments determined by the input in nseg is selected; if large=TRUE this will be the nseg segments with the highest variance, whereas if large=FALSE the subset will consist of the nseg segments with the lowest variance.

If what="length" selection is based on the genomic length of the segments (end position minus start position). If thres is specified, the subset of segments for which the length is above (if large=TRUE) or below (if large=FALSE) this threshold is returned. If thres is left unspecified, a given number of segments determined by the input in nseg is selected; if large=TRUE this will be the nseg longest segments, whereas if large=FALSE it will be the nseg shortest segments.

If what="aberration" the aberration frequency is used to select the subset of segments. If thres is specified, the proportion of samples for which the segment value is above (if large=TRUE) or below (if large=FALSE) the threshold is calculated for each segment. The subset of segments where this frequency is above or equal to the proportion set by the parameter p is returned. If thres is not specified, the nseg segments with the highest (1-p)-quantile (if large=TRUE) or the lowest p-quantile (if large=FALSE) is returned.

Value

A list containing:

sel.seg

data frame containing the selected segments.

In addition, depending on the value of what:

seg.var	a vector giving the variance for each segment. Only returned if what = "variance".
seg.length	a vector giving the length of each segment. Only returned if what = "length".
seg.ab.prop	a vector giving the aberration proportion for each segment. Only returned if what = "aberration" and thres is specified.
seg.quantile	a vector giving the (1-p)- or p-quantile for each segment. Only returned if what = "aberration" and thres=NULL.

Author(s)

Gro Nilsen

See Also

multipcf

Examples

#Lymphoma data
data(lymphoma)

#Run multipcf
segments <- multipcf(lymphoma,gamma=12)

#Select the 10 segments with the highest variance:
sel.seg1 <- selectSegments(segments)

#Select the segments where the variance is below 0.001
sel.seg2 <- selectSegments(segments,thres=0.001,large=FALSE)

#Select the 5 longest segments:
sel.seg3 <- selectSegments(segments,what="length",nseg=5)

#Select the segments where 20 % of the samples have segment value of 0.2 or more:
sel.seg4 <- selectSegments(segments,what="aberration",thres=0.2,p=0.2)

#Select the 20 segments with the largest median:
sel.seg5 <- selectSegments(segments,what="aberration",nseg=20,p=0.5)

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

multipcf finished for chromosome arm 1p 
multipcf finished for chromosome arm 1q 
multipcf finished for chromosome arm 2p 
multipcf finished for chromosome arm 2q 
multipcf finished for chromosome arm 3p 
multipcf finished for chromosome arm 3q 
multipcf finished for chromosome arm 4p 
multipcf finished for chromosome arm 4q 
multipcf finished for chromosome arm 5p 
multipcf finished for chromosome arm 5q 
multipcf finished for chromosome arm 6p 
multipcf finished for chromosome arm 6q 
multipcf finished for chromosome arm 7p 
multipcf finished for chromosome arm 7q 
multipcf finished for chromosome arm 8p 
multipcf finished for chromosome arm 8q 
multipcf finished for chromosome arm 9p 
multipcf finished for chromosome arm 9q 
multipcf finished for chromosome arm 10p 
multipcf finished for chromosome arm 10q 
multipcf finished for chromosome arm 11p 
multipcf finished for chromosome arm 11q 
multipcf finished for chromosome arm 12p 
multipcf finished for chromosome arm 12q 
multipcf finished for chromosome arm 13q 
multipcf finished for chromosome arm 14q 
multipcf finished for chromosome arm 15q 
multipcf finished for chromosome arm 16p 
multipcf finished for chromosome arm 16q 
multipcf finished for chromosome arm 17p 
multipcf finished for chromosome arm 17q 
multipcf finished for chromosome arm 18p 
multipcf finished for chromosome arm 18q 
multipcf finished for chromosome arm 19p 
multipcf finished for chromosome arm 19q 
multipcf finished for chromosome arm 20p 
multipcf finished for chromosome arm 20q 
multipcf finished for chromosome arm 21q 
multipcf finished for chromosome arm 22q 
multipcf finished for chromosome arm 23p 
multipcf finished for chromosome arm 23q 

copynumber documentation built on Nov. 8, 2020, 6:10 p.m.