perm.for.cutoff2: Function that permutes the dataset and finds an appropriate...

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

Description

Function that permutes the dataset and finds an appropriate cutoff value. (Compatible with Vamsee's run.all.lms)

Usage

perm.for.cutoff2(permutations = 100, tx_expr, cov, gene.ids, SCORE,
  num.cores = 10)

Arguments

tx_expr	Expression matrix in form: [genes x samples]. Will be converted to a list(!) of gene-expr vectors (if not input as list)
cov	Regression covariates [cov x samples]
gene.ids	Character vector of gene IDs, corresponding to rows in 'tx_expr' [genes x samples]
SCORE	Main covariate to be permuted (not included in 'cov')
num.cores	The number of cores you would like to use

Value

A 95

Examples

perm.results <- perm.for.cutoff2(permutations = 100, my.list[[1]], my.list[[2]], my.list[[3]], my.list[[4]])

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