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Correct Copy Ratio File if GATK and Pipeline Gender Disagree

Source: R/CNVplot.R
CorrectGender.Rd

Adjusts the X chromosome log2 copy ratio in the coverage data if the gender assigned by GATK and the pipeline do not match.

Usage

CorrectGender(cov, seg)

Arguments

cov

Data frame or tibble. Coverage data, must include columns CONTIG and LOG2_COPY_RATIO.

seg

Data frame or tibble. Segmentation data, must include columns gatk_gender and pipeline_gender.

Value

The corrected coverage data frame or tibble.

Details

  • If GATK gender is "male" and pipeline gender is "female", subtracts 1 from X chromosome log2 copy ratio.

  • If GATK gender is "female" and pipeline gender is "male", adds 1 to X chromosome log2 copy ratio.

  • Otherwise, returns the input coverage unchanged.

Examples

# CorrectGender(cov, seg)