carma.all: Calculate CARMA scores within a region

In arnevpladsen/CARMA: Calculate CARMA scores

Description

This function will not be called directly by the user. The function is used by the CARMA function to calculate CARMA scores within one predefined region. It returns six numerical values, corresponding to the six different CARMA scores

Usage

carma.all(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 functions calculating AMP and DEL 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 vector giving the 6 CARMA scores.

Examples

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

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