StackPlot: StackPlot

Description Usage Arguments Details Value Author(s) Source Examples

View source: R/StackPlot.R

Description

Stackplot: Produces stacked plots of CNV calls from multiple samples for a given locus.

Usage

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StackPlot(Pos, IDs, PathRawData, CNVs, Highlight = NULL, SNPList = NULL,
  key = NA, OutFolder = ".", Files = NA, Pattern = "",
  recursive = FALSE)

Arguments

Pos:

Position of the loci to plot in the form chr21:1050000-1350000.

IDs:

List of IDs to plot

PathRawData:

The path to the raw data files contining LRR and BAF values to plot.

CNVs:

Data frame containing the CNVs called on the samples.

Highlight:

Position of a specific region to be highlighted, in the form chr21:1050000-1350000, default = NULL.

SNPList:

Getting chromosome (chr) and position from another source than the RawFile - input should be the full path of the SNPList with columns: Name, Chr, and Position. Any positions from the RawFile will be erased. A PFB-column is also allowed but will be overwritten by the PFB-parameter or exchanged with 0.5, default = NULL.

key:

Exchange the ID printed on the plot with a deidentified ID - requires that the CNV data frame contains a column called ID_deidentified, default = NA.

OutFolder:

Path for saving outputfiles. Default is current folder

Files:

Full path for each sample. You can get it using the command: Files <- list.files(path=PathRawData, pattern=Pattern, full.names=TRUE, recursive=FALSE). Then use Files=Files.

Pattern:

File pattern in the raw data, default = "*".

Recursive:

Logical, Should files matching patterns in subfolders be included, default = FALSE.

Details

For each sample two tracks are plotted representing the Log R Ratio (LRR) and the B Allele Frequency (BAF).

Value

A png plot of the specified loci.

Author(s)

Johan Hilge Thygesen, Ida Elken Sønderby, Louise K. Hoeffding.

Source

http://biopsych.dk/iPsychCNV

Examples

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mockCNV <- MockData(N=5, Type="Blood", Cores=1)
cnvs <- iPsychCNV(PathRawData=".", Cores=1, Pattern="^MockSample*", Skip=0)
StackPlot(Pos="chr21:28338230-46844965", IDs=unique(cnvs$ID), PathRawData=".", CNVs=cnvs, Highlight = "chr21:36653812-39117308")

mbertalan/iPsychCNV documentation built on June 30, 2017, 2:02 a.m.