correctReadDepth {TitanCNA} | R Documentation

## Correct GC content and mappability biases in sequencing data read counts

### Description

Correct GC content and mappability biases in tumour sequence read counts using Loess curve fitting. Wrapper for function in HMMcopy.

### Usage

      correctReadDepth(tumWig, normWig, gcWig, mapWig,
      			genomeStyle = "NCBI", targetedSequence = NULL)

### Arguments

`tumWig` | File path to fixedStep WIG format file for the tumour sample. See `wigToRangedData` in the HMMcopy for more details.
`normWig` | File path to fixedStep WIG format file for the normal sample.
`gcWig` | File path to fixedStep WIG format file for the GC content based on the specific reference genome sequence used.
`mapWig` | File path to fixedStep WIG format file for the mappability scores computed on the specific reference genome used.
`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.
`targetedSequence` | data.frame with 3 columns: chr, start position, stop position. Use this argument for exome capture sequencing or targeted deep sequencing data. This is experimental and may not work as desired.

### Details

Wrapper for `correctReadcount` in HMMcopy package. It uses a sampling of 50000 bins to find the Loess fit. Then, the log ratio for every bin is returned as the log base 2 of the ratio between the corrected tumour read count and the corrected normal read count.

### Value

`data.frame` containing columns:

`chr` | Chromosome; uses 'X' and 'Y' for sex chromosomes
`start` | Start genomic coordinate for bin in which read count is corrected
`end` | End genomic coordinate for bin in which read count is corrected
`logR` | Log ratio, log2(tumour:normal), for bin in which read count is corrected

### Author(s)

Gavin Ha <gavinha@gmail.com>, Daniel Lai <jujubix@cs.ubc.ca>, Yikan Wang <ykwang@bccrc.ca>

### References

Ha, G., Roth, A., Lai, D., Bashashati, A., Ding, J., Goya, R., Giuliany, R., Rosner, J., Oloumi, A., Shumansky, K., Chin, S.F., Turashvili, G., Hirst, M., Caldas, C., Marra, M. A., Aparicio, S., and Shah, S. P. (2012). Integrative analysis of genome wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer. Genome Research, 22(10):1995,2007. (PMID: 22637570)

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)

### See Also

`correctReadcount` and `wigToRangedData` in the HMMcopy package. WIG: http://genome.ucsc.edu/goldenPath/help/wiggle.html

### Examples

    tumWig <- system.file("extdata", "test_tum_chr2.wig", package = "TitanCNA")
    normWig <- system.file("extdata", "test_norm_chr2.wig", package = "TitanCNA")
    gc <- system.file("extdata", "gc_chr2.wig", package = "TitanCNA")
    map <- system.file("extdata", "map_chr2.wig", package = "TitanCNA")

    #### GC AND MAPPABILITY CORRECTION ####
    cnData <- correctReadDepth(tumWig, normWig, gc, map)

[Package TitanCNA version 1.28.0 Index]