prepAscat_t: Prepare input files for ASCAT tumor only samples

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Prepare input files for ASCAT tumor only samples

Description

Function takes the output from gtMarkers and generates 'logR' and 'BAF' files required for ASCAT analysis.

Usage

prepAscat_t(t_counts = NULL, sample_name = NA, min_depth = 15)

Arguments

t_counts	read counts from tumor generated by gtMarkers
sample_name	Sample name. Used as a basename for output files. Default NA, parses from 't_counts' file.
min_depth	Min read depth required to consider a marker. Default 15

Details

The function will filter SNPs with low coverage (default <15), estimate BAF, logR, and generates the input files for ASCAT. Tumor 'logR' file will be normalized for median depth of coverage. Alternatively, logR file can be segmented with segmentLogR

Value

Generates logR and BAF files required by ASCAT

References

Van Loo P, Nordgard SH, Lingjærde OC, et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A. 2010;107(39):16910-16915. doi:10.1073/pnas.1009843107

See Also

gtMarkers prepAscat segmentLogR

PoisonAlien/maftools documentation built on April 7, 2024, 2:49 a.m.