gen.tab: gen.tab

In margarethannum/gnomeR: What the Package Does (One Line, Title Case)

Description

Creates a summary table of the distribution of the genetic features by a specific outcome/covariate of interest. The difference is tested using Fisher's exact test and further adjusted for multiple comparisons. Note that continuous genetic factors are dichotomized at their median.

Usage

gen.tab(gen.dat, outcome, filter = 0, paired = F, cont = F,
  rank = T)

Arguments

gen.dat	A matrix or dataframe, with patients as rows and features as columns.
outcome	A leveled vector of length equal to the number of rows in gen.dat.
filter	a numeric value between 0 and 1 (1 not included) that is the lower bound for the proportion of patients having a genetic event (only for binary features). All features with an event rate lower than that value will be removed. Default is 0 (all features included).
paired	Boolean if the data are paired. Default is FALSE.
cont	Should the outcome be treated as a continuous value. Default is FALSE treated as categorical.
rank	Should the table returned be oredered by Pvalue. Boolean, default is T

Value

fits : a table of odds ratio and pvalues.

forest.plot : A forest plot of the top 10 hits.

Examples

library(gnomeR)
patients <- unique(clin$DMPID)[1:500]
mut.only <- create.bin.matrix(patients = patients,maf = mut)
gen.dat <- mut.only$mut
outcome = as.factor(as.character(clin$Sex[match(patients,clin$DMPID)]))
test <- gen.tab(gen.dat,outcome)
head(test$fits)
test$forest.plot

margarethannum/gnomeR documentation built on Feb. 26, 2020, 8:16 p.m.