lm_count_mat_perm_pval: Wrapper function for permutation differential expression...

In nkurniansyah/Olivia: RNA-seq Analysis

Wrapper function for permutation differential expression analysis

Description

The function is to calculate DEG (Differential Expression Genes) analysis for selected genes using multiple residual permuation results as outcome to calucate permutation p-value

Usage

lm_count_mat_perm_pval(
  count_matrix,
  pheno,
  trait,
  covariates_string,
  n_permute = 1e+05,
  gene_IDs = NULL,
  log_transform = "log_replace_half_min",
  seed = NULL,
  outcome_type = "continuous"
)

Arguments

count_matrix	A matrix of gene counts (possibly transformed). rows are genes, columns are individuals
pheno	A data frame of phenotype data, includes the trait and covariates.
trait	A character, the name of the exposure variable. The trait should be a column in pheno.
covariates_string	A character string with specifying the covariats, include "as.factor" statements. example: covariate_string = "Age+as.factor(Sex)"
n_permute	Number of permutation. Default is 100000 times
gene_IDs	A vector of selection of geneID, NULL if all genes are tested
log_transform	One of the transformations log_replace_half_min, log_add_min, log_add_0.5, or NULL (default)
seed	Random seed
outcome_type	continuous and binary. Default is continuous

Value

Linear regression results as a data frame with columns GeneID, beta,se,t_stat (t-statistic), t_stat_df(degree of freedom),p_value, perm_pval

Examples

library(dplyr)
data(rnaseq_count_matrix)
data(phenotype)
rnaseq_count_matrix<- rnaseq_count_matrix[rowSums(rnaseq_count_matrix)>0,]
genes<-c("ENSG00000000003","ENSG00000000005","ENSG00000000419","ENSG00000000457","ENSG00000000460")
covariates_string<-"Age+Sex"
trait<-"Trait.1"
lm_count_mat_perm_pval(count_matrix=rnaseq_count_matrix, pheno=phenotype,
                       trait=trait, covariates_string= covariates_string,
                       gene_IDs=genes,n_permute=1000,
                       log_transform = "log_replace_half_min",
                       seed = NULL)

nkurniansyah/Olivia documentation built on July 29, 2023, 9:10 a.m.