R: Calculate and plot correlation of region read counts among...
plotAndCalculateCorrelationDatasets
R Documentation
Calculate and plot correlation of region read counts among pairs of input files.
Description
plotAndCalculateCorrelationDatasets calculates and plots the pairwise correlation of all pairs of input files with among each other.
The main purpose is to identify artefacts with particular files that should subsequently be excluded.
The correlation is based on the raw region read counts(i.e., before binning).
The results of the correlation analysis are stored in the SNPhood object.
If the corrplot package is available, it will be used to produce a nice visualization of the correlation matrix.
Character(1) or NULL. Default NULL.
Filename of the PDF file for the output plots.
If set to NULL, plots will be plotted to the currently active device.
corMeasure
Character(1). Default "pearson". The correlation measure that should be used to compare between pairs of samples.
Either pearson, spearman, or kendall.
verbose
Logical(1). Default FALSE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?
...
Additional arguments for the corrplot.mixed function from the corrplot package (if available).
Value
An object of type SNPhood, with the results of the correlation analysis stored in the slot "additionalResults".
They can be retrieved via the helper function results for further investigation.
The results consist of a named list with two elements: A correlation matrix of the region read counts across all input files and a
translation table to correlate the input files with the abbreviations from the correlation plot.
Examples
data(SNPhood.o, package="SNPhood")
# Plot directly, using Pearson correlation
SNPhood.o = plotAndCalculateCorrelationDatasets(SNPhood.o)
# Plot to a PDF file
SNPhood.o = plotAndCalculateCorrelationDatasets(SNPhood.o, fileToPlot = "res.pdf")
# Using Spearman correlation instead of Pearson
SNPhood.o = plotAndCalculateCorrelationDatasets(SNPhood.o, corMeasure = "spearman")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(SNPhood)
Loading required package: GenomicRanges
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:GenomicRanges':
shift
The following object is masked from 'package:IRanges':
shift
Loading required package: checkmate
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| Welcome to the SNPhood package and thank you for using our software. This is SNPhood version 1.2.2. |
| See the vignettes (type browseVignettes("SNPhood") or the help pages for how to use SNPhood for your analyses. |
| Thank you for using our software. Please do not hesitate to contact us if there are any questions. |
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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPhood/plotAndCalculateCorrelationDatasets.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotAndCalculateCorrelationDatasets
> ### Title: Calculate and plot correlation of region read counts among pairs
> ### of input files.
> ### Aliases: plotAndCalculateCorrelationDatasets
>
> ### ** Examples
>
> data(SNPhood.o, package="SNPhood")
> # Plot directly, using Pearson correlation
> SNPhood.o = plotAndCalculateCorrelationDatasets(SNPhood.o)
> # Plot to a PDF file
> SNPhood.o = plotAndCalculateCorrelationDatasets(SNPhood.o, fileToPlot = "res.pdf")
> # Using Spearman correlation instead of Pearson
> SNPhood.o = plotAndCalculateCorrelationDatasets(SNPhood.o, corMeasure = "spearman")
>
>
>
>
>
> dev.off()
null device
1
>