seqplots (version 1.10.2)

getPlotSetArray: Process genomic signal

Description

Function to process genomic signal from tracks and/or motif data, calculate statistics. This function should be used as the entry point to the SeqPlots pipeline and followed by plotting function(s).

Usage

getPlotSetArray(tracks, features, refgenome, bin = 10L, rm0 = FALSE,
  ignore_strand = FALSE, xmin = 2000L, xmax = 2000L, xanchored = 1000L,
  type = "pf", add_heatmap = TRUE, verbose = FALSE, stat = "mean",
  lvl1m = message, lvl2m = message)

Arguments

tracks

Character vector or list of BigWig track paths. For motif density plots MotifSetup class containing motifs setup and/or BigWig track paths (see details)

features

Character vector or list containing feature file paths (BED or GFF).

refgenome

The UCSC code of reference genome, e.g. 'hg19' for Homo sapiens (see details)

bin

Binning window size in base pairs, defaults to 1L

rm0

Remove zeros from mean/error estimate calculation, 0 in track file will be treated as missing data, defaults to FALSE

ignore_strand

If TRUE the directionality is ignored, that is all features' strands, regardless of annotation in GFF/BED file, are treated as undetermined ("*"), defaults to FALSE

xmin

Upstream calculation distance in base pairs, defaults to 200L

xmax

Downstream calculation distance in base pairs, defaults to 2000L

xanchored

Anchored, feature body pseudo length in base pairs. The features will be extended or shrunk using linear approximation. Used only if /code{type="af"}, defaults to 1000L

type

The type of the calculation, "pf" for point features (default), "mf" for midpoint features, "ef" for endpoint features and "af" for anchored features, see details

add_heatmap

Add the heatmap data to output, must be on to plot heatmap form output PlotSetArray class, defauls to TRUE

verbose

Print various messages and warnings, defaults to FALSE

stat

If set to "median" the median is used as summarizing statistic for linear plots instead of mean

lvl1m

function to handle lvl 1 messages, useful when invoked in Shiny GUI environment, defaults to message

lvl2m

function to handle lvl 2 messages, useful when invoked in Shiny GUI environment, defaults to message

Value

• The PlotSetArray object.

Details

This function takes genomic coordinates in BED or GFF format, and extracts the signal from track files (BigWig) and/or calculates motif density in these regions. Then it computes the statistics required for average and heatmap plots. Returns the PlotSetArray class, which can be further subsisted, and used for plotting.

Modes of operation{ The function operate in three modes, determined by type parameter:

• Point Features- anchor plot on the start of a feature. By default, plot will be directional if strand information is present (i.e, use start position and plot on positive strand for + strand features and use end position and plot on negative strand for minus strand features). If strand information is not present in the feature file (or if the "ignore strand" option is chosen), plot will use start position of feature and be plotted on the positive strand (see explanations). User chooses length of upstream and downstream sequence to plot.
• Midpoint Features- similar to point feature, but plot is centred on the midpoint of the feature.
• Endpoint Features- similar to point feature, but plot is centred on the end point (most downstream) of the feature.
• Anchored Features- features are anchored at start and stop positions and given pseudo-length chosen by the user. Additionally, the user chooses the length of sequence upstream of the start and downstream of the end to plot.

}

Binning the track{ bin numeric parameter determines the resolution of data acquisition. The default value 10 means that 10bp intervals within the plotting range will be summarized by calculating the mean. Higher values increases the speed of calculation and produces smoother plots, but decreases resolution. }

DNA motifs{ The MotifSetup class allows to calculate and plot the density of any user-defined motif around the chosen genomic feature using the reference sequence package. Motif plots can be mixed with track files' signal plots. The MotifSetup can be initialized in following way:

ms <- MotifSetup() ms$addMotif("TATA", window=200L, heatmap=TRUE, revcomp=TRUE, name=pattern) ms$addMotif("GAGA", window=100L)$addBigWig("path/to/file.bw") The addMotiff methods accepts following parameters: [object Object],[object Object],[object Object],[object Object],[object Object] }

Reference genomes{ The refgenome parameter determines the reference genome to be used chromosome naming convention (e.g. chrX vs. X) and chromosome lengths. Also for motif plots the genomic sequence is used to calculate motif density tracks. To check which genomic packages are installed in current R session use installed.genomes function. available.genomes gives the list of all reference genome packages currently supplied by BioConductor. Please refer to BSgenome package documentation for installing and forging new genome packages. }

See Also

Other plotting.functions: plotAverage, plotHeatmap, plot

Examples

# Get the paths of example files                      
bed1 <- system.file("extdata", 
    "Transcripts_ce10_chrI_100Kb.bed", package="seqplots")
bed2 <- system.file("extdata", 
    "GSM1208361_chrI_100Kb_PeakCalls.bed", package="seqplots")
bw1 <- system.file("extdata", 
    "GSM1208360_chrI_100Kb_q5_sample.bw", package="seqplots")

#If required install C. elegans genomic package from Bioconductor
if(!"BSgenome.Celegans.UCSC.ce10" %in% BSgenome::installed.genomes()) {
    if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
        source("http://bioconductor.org/biocLite.R")
        biocLite("BSgenome.Celegans.UCSC.ce10")
    }
}

#Get getPlotSetArray for track and feature files
#Does not work on Windows i386 (32 bit)
if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
    plotset1 <- getPlotSetArray(bw1, c(bed1, bed2), 'ce10')
} else {
    load(system.file("extdata", "precalc_plotset.Rdata", package="seqplots"))
}
plot(plotset1) #Average plot
plot(plotset1[1,], what='h') #Heatmap

#Get getPlotSetArray for motifs, track and feature files
ms <- MotifSetup()
ms <- MotifSetup()
ms$addMotif('GAGA')
ms$addMotif('TATA')
ms$addBigWig(bw1)
if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
    plotset2 <- getPlotSetArray(ms, c(bed1, bed2), 'ce10')
}
plot(plotset2) #Average plot
plot(plotset2[1,], what='h') #Heatmap