seqCNA (version 1.18.0)

seqsumm_HCC1143: 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)