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Last data update: 2014.03.03

R: Estimate allelic frequency distributions in bins along the...

binnedAFs

R Documentation

Estimate allelic frequency distributions in bins along the genome

Description

This function is used to give estimates of the ditribution of observed allelic freuqencies in a regions of the genome, use in conjunction with h5dapply

Usage

binnedAFs(data, sampledata, normalise = TRUE, binWidth = 0.05, minCov = 10, minCount = 2)

Arguments

`data`	A `list` object returned by a call to `h5dapply` or `h5readBlock`.
`sampledata`	Sample metadata describing the cohort, can be extracted from an HDF5 tally file using the `getSampleData` function.
`normalise`	Boolean flag to specify whether the counts or percentages of observed allelic frequencies should be returned.
`binWidth`	Width of bins in allelic frequency space, defaults to 0.05.
`minCov`	Minimum required coverage for a position to be considered.
`minCount`	Minimum required number of mismatches for a position to be considered.

Value

A matrix of AF bins times samples.

Author(s)

Paul Theodor Pyl

Examples

library(h5vc)
tallyFile <- system.file( "extdata", "example.tally.hfs5", package = "h5vcData" )
sampleData <- getSampleData( tallyFile, "/ExampleStudy/16" )
afs <- h5dapply(
  filename = tallyFile,
  group = "/ExampleStudy/16",
  names = c("Counts", "Coverages"),
  range = c(29e6, 29.05e6),
  blocksize = 1e4,
  FUN = binnedAFs,
  sampledata = sampleData
)
afs[[3]]

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.
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Type 'license()' or 'licence()' for distribution details.

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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(h5vc)
Loading required package: grid
Loading required package: gridExtra
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/h5vc/binnedAFs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: binnedAFs
> ### Title: Estimate allelic frequency distributions in bins along the
> ###   genome
> ### Aliases: binnedAFs
> 
> ### ** Examples
> 
> library(h5vc)
> tallyFile <- system.file( "extdata", "example.tally.hfs5", package = "h5vcData" )
> sampleData <- getSampleData( tallyFile, "/ExampleStudy/16" )
> afs <- h5dapply(
+   filename = tallyFile,
+   group = "/ExampleStudy/16",
+   names = c("Counts", "Coverages"),
+   range = c(29e6, 29.05e6),
+   blocksize = 1e4,
+   FUN = binnedAFs,
+   sampledata = sampleData
+ )
> afs[[3]]
     PT5ControlDNA PT5PrimaryDNA PT5RelapseDNA PT8ControlDNA PT8EarlyStageDNA
0.05   0.432330827   0.691056911    0.00000000   0.536312849      0.550943396
0.1    0.406015038   0.241869919    0.50847458   0.318435754      0.332075472
0.15   0.082706767   0.036585366    0.28813559   0.078212291      0.049056604
0.2    0.022556391   0.004065041    0.03389831   0.030726257      0.007547170
0.25   0.007518797   0.002032520    0.00000000   0.008379888      0.011320755
0.3    0.000000000   0.000000000    0.00000000   0.000000000      0.003773585
0.35   0.003759398   0.004065041    0.00000000   0.000000000      0.003773585
0.4    0.011278195   0.002032520    0.00000000   0.000000000      0.000000000
0.45   0.015037594   0.000000000    0.00000000   0.000000000      0.007547170
0.5    0.003759398   0.000000000    0.01694915   0.002793296      0.015094340
0.55   0.007518797   0.002032520    0.00000000   0.002793296      0.007547170
0.6    0.003759398   0.000000000    0.03389831   0.002793296      0.000000000
0.65   0.003759398   0.000000000    0.00000000   0.000000000      0.011320755
0.7    0.000000000   0.000000000    0.00000000   0.000000000      0.000000000
0.75   0.000000000   0.000000000    0.00000000   0.000000000      0.000000000
0.8    0.000000000   0.000000000    0.00000000   0.000000000      0.000000000
0.85   0.000000000   0.000000000    0.00000000   0.000000000      0.000000000
0.9    0.000000000   0.002032520    0.00000000   0.000000000      0.000000000
0.95   0.000000000   0.002032520    0.01694915   0.000000000      0.000000000
1      0.000000000   0.012195122    0.10169492   0.019553073      0.000000000
     PT8PrimaryDNA
0.05    0.00000000
0.1     0.20895522
0.15    0.31343284
0.2     0.19402985
0.25    0.05970149
0.3     0.04477612
0.35    0.00000000
0.4     0.07462687
0.45    0.02985075
0.5     0.02985075
0.55    0.01492537
0.6     0.02985075
0.65    0.00000000
0.7     0.00000000
0.75    0.00000000
0.8     0.00000000
0.85    0.00000000
0.9     0.00000000
0.95    0.00000000
1       0.00000000
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>