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Last data update: 2014.03.03

R: Function to load tumour allele counts from a text file or...

loadAlleleCounts

R Documentation

Function to load tumour allele counts from a text file or data.frame

Description

Function to load in the allele counts from tumour sequencing data from a delimited text file or data.frame object.

Usage

  loadAlleleCounts(inCounts, symmetric = TRUE, genomeStyle = "NCBI", sep = "\t", header = TRUE)

Arguments

`inCounts`	Full file path to text file or data.frame containing tumour allele count data. `inCounts` must be 6 columns: chromosome, position, reference base, reference read counts, non-reference base, non-reference read counts. ‘chromosome’ column can be in ‘NCBI’ or ‘UCSC’ genome style; only autosomes, sex chromosomes, and mitochondrial chromosome are included (e.g. 1-22,X,Y,MT). The reference and non-reference base columns can be any arbitrary character; it is not used by TitanCNA.
`symmetric`	`logical`; if `TRUE`, then the symmetric allelic counts will be used. `ref` will equal `max(ref,nonRef)`. This parameter must be the same as the `symmetric` parameter for `loadDefaultParameters`.
`genomeStyle`	The genome style to use for chromosomes by TitanCNA. Use one of ‘NCBI’ or ‘UCSC’. It does not matter what style is found in `inCounts`, `genomeStyle` will be the style returned.
`sep`	Character indicating the delimiter used for the columns for `infile`. Default is tab-delimited, "\t".
`header`	`logical` to indicate if the input tumour counts file contains a header line.

Value

list containing components for

`chr`	Chromosome; character, NCBI or UCSC genome style format
`posn`	Position; integer
`ref`	Reference counts; numeric
`nonRef`	Non-reference counts; numeric
`tumDepth`	Tumour depth; numeric

Author(s)

Gavin Ha <gavinha@gmail.com>

References

Ha, G., Roth, A., Khattra, J., Ho, J., Yap, D., Prentice, L. M., Melnyk, N., McPherson, A., Bashashati, A., Laks, E., Biele, J., Ding, J., Le, A., Rosner, J., Shumansky, K., Marra, M. A., Huntsman, D. G., McAlpine, J. N., Aparicio, S. A. J. R., and Shah, S. P. (2014). TITAN: Inference of copy number architectures in clonal cell populations from tumour whole genome sequence data. Genome Research, 24: 1881-1893. (PMID: 25060187)

Examples

  infile <- system.file("extdata", "test_alleleCounts_chr2.txt", 
                        package = "TitanCNA")
  #### LOAD DATA FROM TEXT FILE ####
  data <- loadAlleleCounts(infile, symmetric = TRUE, 
  		genomeStyle = "NCBI", header = TRUE)
  
  ## Not run: 
	countsDF <- extractAlleleReadCounts(tumBam, tumBamIndex, 
			germlineHetPosns, outputFilename = NULL, 
			pileupParam = PileupParam())
	data <- loadAlleleCounts(countsDF, symmetric = TRUE, 
  			genomeStyle = "NCBI")
  
## End(Not run)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(TitanCNA)
Loading required package: foreach
Loading required package: IRanges
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TitanCNA/loadAlleleCounts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: loadAlleleCounts
> ### Title: Function to load tumour allele counts from a text file or
> ###   data.frame
> ### Aliases: loadAlleleCounts
> ### Keywords: IO
> 
> ### ** Examples
> 
>   infile <- system.file("extdata", "test_alleleCounts_chr2.txt", 
+                         package = "TitanCNA")
>   #### LOAD DATA FROM TEXT FILE ####
>   data <- loadAlleleCounts(infile, symmetric = TRUE, 
+   		genomeStyle = "NCBI", header = TRUE)
titan: Loading data /home/ddbj/local/lib64/R/library/TitanCNA/extdata/test_alleleCounts_chr2.txt
>   
>   ## Not run: 
> ##D 	countsDF <- extractAlleleReadCounts(tumBam, tumBamIndex, 
> ##D 			germlineHetPosns, outputFilename = NULL, 
> ##D 			pileupParam = PileupParam())
> ##D 	data <- loadAlleleCounts(countsDF, symmetric = TRUE, 
> ##D   			genomeStyle = "NCBI")
> ##D   
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>