ttest: Perform two independent sample t test

In MalathiSIDona/pathDESeq: Pathway-Based Differential Expression Analysis for RNA-Seq Data

Description

Function will perform two independent sample t test (two-sided) and will return t test statistics and p values.

Usage

ttest(data, m, n,sig=0.05)

Arguments

data	A data frame which consists the gene expression data. First m columns correspond to the control group and next n columns correspond to the treatment group. Each row represents the gene expression data for a particular gene.
m	Number of replicates for the control group.
n	Number of replicates for the treatment group.
sig	The level of significance. The default value is 0.05.

Details

pathDESeq package uses this function as a internal function for the pgbmrfICM function.

Value

This function will result a data frame contains t test statistics and p values.

Author(s)

Malathi S.I. Dona

See Also

pgbmrfICM

Examples

#load a data frame with 1065 observations for 21 variables.
#First column represents gene names. The next 10 columns correspond to the control group and
#last 10 columns correspond to the treatment group. Each row represents gene expression data
#- for a particular gene.
data("data1065")

#store gene expression data
data<-data1065[,-1]

#take m=10 and n=10 as replicates for groups

#perform t test at 5% significance level for 1065 genes
t.test.results<-ttest(data=data,m=10,n=10)

head(t.test.results)

MalathiSIDona/pathDESeq documentation built on May 8, 2019, 3:37 p.m.