toDNAcopyObj: Function to create a DNAcopy object for plot functions.

In fastseg: fastseg - a fast segmentation algorithm

Description

Function to create a DNAcopy object for plot functions.

Usage

  toDNAcopyObj(segData, chrom, maploc, genomdat,
    sampleNames)

Arguments

segData	The results of the segmentation.
chrom	The vector of the chromosomes from the original data.
maploc	A vector with the physical positions of the original data.
genomdat	A matrix with the original data.
sampleNames	The sample names of the original data.

Value

An DNAcopy equivalent object.

Author(s)

Andreas Mitterecker

Examples

library(fastseg)

#####################################################################
### the data
#####################################################################
data(coriell)
head(coriell)

samplenames <- colnames(coriell)[4:5]
data <- as.matrix(coriell[4:5])
data[is.na(data)] <- median(data, na.rm=TRUE)
chrom <- coriell$Chromosome
maploc <- coriell$Position


###########################################################
## GRanges
###########################################################

library("GenomicRanges")

## with both individuals
gr <- GRanges(seqnames=chrom,
        ranges=IRanges(maploc, end=maploc))
mcols(gr) <- data
colnames(mcols(gr)) <- samplenames
res <- fastseg(gr)

segres <- toDNAcopyObj(
        segData     = res,
        chrom       = as.character(seqnames(gr)),
        maploc      = as.numeric(start(gr)),
        genomdat    = data,
        sampleNames = samplenames)

## with one individual
gr2 <- gr
data2 <- as.matrix(data[, 1])
colnames(data2) <- "sample1"
mcols(gr2) <- data2
res <- fastseg(gr2)

segres <- toDNAcopyObj(
        segData     = res,
        chrom       = as.character(seqnames(gr)),
        maploc      = as.numeric(start(gr)),
        genomdat    = as.matrix(data2),
        sampleNames = unique(mcols(res)$ID))


###########################################################
## vector
###########################################################
data2 <- data[, 1]
res <- fastseg(data2)
segres <- toDNAcopyObj(
        segData     = res,
        chrom       = rep(1, length(data2)),
        maploc      = 1:length(data2),
        genomdat    = as.matrix(data2),
        sampleNames = "sample1")


###########################################################
## matrix
###########################################################
data2 <- data[1:400, ]
res <- fastseg(data2)
segres <- toDNAcopyObj(
        segData     = res,
        chrom       = rep(1, nrow(data2)),
        maploc      = 1:nrow(data2),
        genomdat    = as.matrix(data2),
        sampleNames = colnames(data2))



#####################################################################
### plot the segments
#####################################################################

library(DNAcopy)
plot(segres)

Example output

Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

        Clone Chromosome Position Coriell.05296 Coriell.13330
1  GS1-232B23          1        1      0.000359      0.207470
2  RP11-82d16          1      469      0.008824      0.063076
3  RP11-62m23          1     2242     -0.000890      0.123881
4  RP11-60j11          1     4505      0.075875      0.154343
5 RP11-111O05          1     5441      0.017303     -0.043890
6  RP11-51b04          1     7001     -0.006770      0.094144

Attaching package: 'DNAcopy'

The following object is masked _by_ '.GlobalEnv':

    coriell

fastseg documentation built on Nov. 8, 2020, 7:46 p.m.