Compute.input.variables: Compute Mutation Counts from Tumor Exome Somatic Mutations

In MSIseq: Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations

Description

This function returns a data frame of mutation counts from the mutation information in the data argument.

Usage

Compute.input.variables(data, repeats, uniform.seq.len=38, seq.len = NULL)

Arguments

data	A data frame in the NGS "mutation annotation file" format. See NGStestdata for details.
repeats	A data frame indicating the genome coordinates of simple sequence repeats.
uniform.seq.len	The length of the capture sequence. This argument should be used when the capture sequences for all the samples have the same length. This argument will be ignored when seq is supplied.
seq.len	A data frame with two columns: Tumor_Sample_Barcode and the corresponding Sequence_Length (Mb). This should be provided if the capture sequences for the tumors have different lengths.

Details

This function computes 9 variables (listed below) from data. Mutations are one of two types: single nucleotide substitutions (SNSs) and short insertions/deletions (indels).

• T.sns: total count of SNSs/Mb

• S.sns: count of SNSs in simple sequence repeats/Mb

• T.ind: total count of indels/Mb

• S.ind: count of indels in simple sequence repeats/Mb

• T: total mutation count/Mb

• S: mutation count in simple sequence repeats/Mb

• ratio.sns: S.sns/T.sns

• ratio.ind: S.ind/T.ind

• ratio: S/T

Value

A data frame with 9 columns that are the 9 variables listed above.

Author(s)

Mini Huang

See Also

MSIseq.train, MSIseq.classify,

Examples

## Not run: 
## load sample data: NGStestdata, NGStestseqLen

data(NGStestdata)
data(NGStestseqLen)

## download the Hg19repeats annotation file and load it
url <- 
"http://steverozen.net/data/Hg19repeats.rda"
file <- basename(url)
download.file(url, file)
load("Hg19repeats.rda")

## get mutation counts for test data 

test.mutationNum<-Compute.input.variables(NGStestdata, 
	repeats=Hg19repeats, seq.len = NGStestseqLen)

## End(Not run)

MSIseq documentation built on May 2, 2019, 7:23 a.m.