seqsumm_HCC1143 {seqCNA} | R Documentation

## Example of a seqsumm output, namely for a sequenced sample of the HCC1143 cancer cell-line.

### Description

The `runSeqsumm` function was run over a SAM file at a summarization window of 200Kbps and only chromosomes 1 to 5 were kept.

### Usage

    data(seqsumm_HCC1143)

### Format

A data frame with 5314 genomic windows on the following 5 variables.

`chrom`

  A numeric vector with the chromosome of the corresponding window.

`win.start`

  A numeric vector with the first zero-based base pair index of the corresponding window.

`reads.gc`

  A numeric vector with the mean GC content for the reads within the corresponding window.

`reads.mapq`

  A numeric vector with the mean mapping quality for the reads within the corresponding window.

`counts`

  A numeric vector with the read count within the corresponding window.

### References

High-resolution mapping of copy-number alterations with massively parallel sequencing. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES. Nature. 2010 Jan; 6(1):99-103

### Examples

    data(seqsumm_HCC1143)
    head(seqsumm_HCC1143)

[Package seqCNA version 1.38.0 Index]