prepAscat: Prepare input files for ASCAT

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

Prepare input files for ASCAT

Description

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

Usage

prepAscat(
  t_counts = NULL,
  n_counts = NULL,
  sample_name = NA,
  min_depth = 15,
  normalize = TRUE
)

Arguments

t_counts	read counts from tumor generated by gtMarkers
n_counts	read counts from normal 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
normalize	If TRUE, normalizes for library size. Default TRUE

Details

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

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_t segmentLogR

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