get.vars: Function that will get the variables you need to run all the...

In syyang93/analyzeR: This package contains functions that Stephanie uses for her analysis of recount RNAseq data.

Description

Function that will get the variables you need to run all the lms in parallel

Usage

get.vars(lm_full, permutevar = "mtDNA_adjust_AGE",
  covnames = c(paste0("PC", 1:10), paste0("Genotyping.PC", 1:3), "sex",
  "COHORT"))

Arguments

lm_full	A data frame with all variables. Column = genes, covariates, etc. Rows = observations (in this case, individuals)
permutevar	The main variable, as a string (for my case, mtDNA-CN)
covnames	Names of the covariates to be included in the regression, a vector of strings.

Value

a list containing tx_expr, cov, gene.ids, and SCORE, all of which are to be fed into the function "run.all.lms"

Examples

my.list <- get.vars.runall.lms(lm_full, permutevar = 'mtDNA_adjust_AGE')

syyang93/analyzeR documentation built on Aug. 26, 2020, 4:34 p.m.