ADAM2.panessprofile: Calculate profile of number of fitness genes across fixed...

In DepMap-Analytics/ADAM2: Adaptive Daisy Model

Description

This function calculates the numbers (and cumulative numbers) of genes whose inactivation exerts a fitness effect in n cell lines, varying n from 1 to the number of cell lines in the dataset in input.

Usage

ADAM2.panessprofile(depMat,
                   display=TRUE,
                   main_suffix='fitness genes in at least 1 cell line',
                   xlab='n. dependent cell lines')

Arguments

depMat	Binary dependency matrix, rows are genes and columns are samples. 1 in position [i,j] indicates that inactivation of the i-th gene exerts a significant loss of fitness in the j-th sample, 0 otherwise.
display	Boolean, default is TRUE. Should bar plots of the dependency profiles be plotted
main_suffix	If display=TRUE, title suffix to give to plot of number of genes depleted in a give number of cell lines, default is 'genes depleted in at least 1 cell line'
xlab	If display=TRUE, label to give to x-axis of the plots, default is 'n. cell lines'

Value

A list with the following two named vectors:

panessprof	Number of genes that are depleted for a number of cell lines
CUMsums	Cumulative number of genes depleted in at least x cell lines

Author(s)

C. Pacini, E. Karakoc & F. Iorio

Examples

data(exampleDepMat)
pprofile <- ADAM2.panessprofile(depMat = exampleDepMat)

DepMap-Analytics/ADAM2 documentation built on Dec. 1, 2019, 12:27 a.m.