carma.S1 2: Calculate CARMA score AMP

In arnevpladsen/CARMA: Calculate CARMA scores

Description

This function will not be called directly by the user. The function is used by the carma.all function to calculate the CARMA score AMP, a measure of the extent of regional gain in copy number.

Usage

carma.S1(seg, ploidy, gender = NULL)

Arguments

seg	a data frame with copy number data corresponing to one region.
ploidy	an integer value corresponding to the median copy number across the whole genome, calculated using the center function.
gender	a character string giving gender. If gender="male", the function will correct for an expected lower value for the X chromosome in segments covering the X chromosome. This is done by dividing the ploidy by 2 when calculating AMP and DEL in these segments.

Value

A numeric score.

Examples

segment <- test.data[[1]]
seg <- segment[segment$chr==1, ] 
ploidy <- center(test.data[[1]])
carma.S1(seg, ploidy)

arnevpladsen/CARMA documentation built on Dec. 19, 2021, 4:39 a.m.