R: Graphically summarize the results of the allelic bias...
plotAllelicBiasResults
R Documentation
Graphically summarize the results of the allelic bias analysis for a specific dataset and region.
Description
plotAllelicBiasResults graphically summarizes the results of the allelic bias analysis for a specific dataset and region.
Three plots are generated, each of which focuses on a different aspect of the allelic bias analysis across the selected user region.
Numeric(1) or Character(1). Single dataset that should be used for plotting, either specified as integer (such as 1, value must be
between 1 and the total number of datasets as defined in the object) or its annotation (name must appear in the dataset names as obtained via the function annotationDatasets).
region
Numeric(1) or Character(1). Single region that should be plotted, either specified as integer (such as 1, value must be
between 1 and the total number of region as defined in the object) or its annotation (name must appear in the region names as obtained via the function annotationRegions).
signThreshold
Numeric(1). Default 0.05. The significance threshold (such as p-value or FDR threshold). Must be between 0 and 1. If the parameter belongs to a plotting function, a horizontal line is drawn at the chosen value. For the allelic bias summary plots, p-values below this threshold and the corresponding allelic fractions are highlighted.
readGroupColors
Character or NULL. Default NULL. Colors of the read groups that appear in the plot.
If set to NULL, colors will be set automatically. The length of the vector must equal the total number of read groups
that are defined in the SNPhood object.
fileToPlot
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.
verbose
Logical(1). Default FALSE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?
Details
The first plot shows the estimates of the allelic fraction, along with confidence intervals for the estimate
according to the parameters chosen when the function testForAllelicBias was called. Fraction estimates for which the corresponding p-values
are deemed significant according to the value of the parameter signThreshold are highlighted (see also the legend). At 0.5, the estimated
allelic fraction if there was no allelic bias, a horizontal line is drawn.
The second plot shows the p-values (-log 10 transformed, so that smaller p-values have higher transformed values).
In analogy to the estimates of the allelic fraction, significant p-values are highlighted. The -log10 transformed significance threshold
(according to the parameter signThreshold) appears as a horizontal line.
Finally, the third plot shows the distribution of the read counts across all read groups. In addition, the genotype distribution for each
read group is given (see the Vignette for details). This helps to identify allelic biases based on genotype differences among read groups.
Value
the generated ggplot2 plot(s) as list for further processing. May contain multiple plots, depending on the function. The plot(s) can then be plotted individually or modified arbitrarily as the user wants. For example, if multiple plots are returned and the plots have been saved in a variable called plots.l, simply type plots.l[[1]] to view the first plot.
Examples
data(SNPhood.o, package="SNPhood")
SNPhood.o = testForAllelicBiases(SNPhood.o, readGroups = c("maternal", "paternal"))
# Leave all parameters with their standard values
plots = plotAllelicBiasResults(SNPhood.o)
# Change the colors
plots = plotAllelicBiasResults(SNPhood.o, readGroupColors = c("blue", "red", "gray"))
# Alter the significance threshold
plots = plotAllelicBiasResults(SNPhood.o, signThreshold = 0.01)
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/plotAllelicBiasResults.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotAllelicBiasResults
> ### Title: Graphically summarize the results of the allelic bias analysis
> ### for a specific dataset and region.
> ### Aliases: plotAllelicBiasResults
>
> ### ** Examples
>
> data(SNPhood.o, package="SNPhood")
> SNPhood.o = testForAllelicBiases(SNPhood.o, readGroups = c("maternal", "paternal"))
Check object integrity and validity. For large objects, this may take some time. Use the function changeObjectIntegrityChecking to disable this check for the object.
Finished execution using 1 cores.
Execution time: 0 secs
Finished execution using 1 cores.
Execution time: 0 secs
Finished execution using 1 cores.
Execution time: 0.2 secs
Finished execution using 1 cores.
Execution time: 0.2 secs
Finished execution using 1 cores.
Execution time: 0 secs
Test allelic bias for dataset GM10847
Calculating read overlaps for the background distribution... This may take a while
Read group maternal
Finished execution using 1 cores.
Execution time: 0.5 secs
Read group paternal
Finished execution using 1 cores.
Execution time: 0.1 secs
Calculate background distribution with 100 repetitions. This may take a while.
Finished execution using 1 cores.
Execution time: 2.6 secs
Test allelic bias for dataset GM12890
Calculating read overlaps for the background distribution... This may take a while
Read group maternal
Finished execution using 1 cores.
Execution time: 0.1 secs
Read group paternal
Finished execution using 1 cores.
Execution time: 0.1 secs
Calculate background distribution with 100 repetitions. This may take a while.
Finished execution using 1 cores.
Execution time: 4 secs
FINISHED SUCCESSFULLY WITH ALLELIC BIAS TEST.
Execution time: 20.3 secs
> # Leave all parameters with their standard values
> plots = plotAllelicBiasResults(SNPhood.o)
Warning message:
Removed 30 rows containing missing values (geom_point).
>
> # Change the colors
> plots = plotAllelicBiasResults(SNPhood.o, readGroupColors = c("blue", "red", "gray"))
Warning message:
Removed 30 rows containing missing values (geom_point).
>
> # Alter the significance threshold
> plots = plotAllelicBiasResults(SNPhood.o, signThreshold = 0.01)
Warning message:
Removed 30 rows containing missing values (geom_point).
>
>
>
>
>
>
> dev.off()
null device
1
>