Groupcomparison {BloodGen3Module}R Documentation

Group comparison analysis

Description

The Groupcomparison function will perform group comparison analyses and the results are expressed “at the module level” as percent of genes increased or decreased.

Usage

Groupcomparison(
  data.matrix,
  sample_info = NULL,
  FC = NULL,
  pval = NULL,
  FDR = TRUE,
  Group_column = NULL,
  Test_group = "Test_group",
  Ref_group = "Control",
  SummarizedExperiment = TRUE
)

Arguments

data.matrix

Matrix of normalized expression data (not Log2 transformed).Row names are required to be valid Gene Symbols. Columns names are sample IDs or data.matrix can also be given a summarizedexperiment object and assigned data.matrix and sample_info accordingly from the object.

sample_info

A dataframe with sample annotation. Sample_info dataframe requires two columns: 1) a column specifying Sample ID (exactly matching the Sample ID of data.matrix) and 2) a column specifying group names

FC

Numeric value specifying the foldchange cut off that will be applied to define increase or decrease of a given transcript compared to the reference group

pval

Numeric value specifying p-value cut off or False discovery rate when FDR = TRUE

FDR

Logical operator to specify whether False discovery rate cut off (using BH-method) should be used

Group_column

Character vector identical to the column name from sample_info dataframe that specifies group annotation used for the analysis

Test_group

Character vector specifying values within the group column (Group_column) that will be used as Test group (samples considered as cases or “intervention” group).

Ref_group

Character vector specifying value within the group column (Group_column) that will be used as Reference group

SummarizedExperiment

Output data as the SummarizedExperiment class when SummarizedExperiment = TRUE

Value

            A matrix of the percentahe of module response in each group comparison

Author(s)

Darawan Rinchai drinchai@gmail.com

Examples

## data could be downloaded from ExperimentHub("GSE13015")
library(ExperimentHub)
library(SummarizedExperiment)
dat = ExperimentHub()
res = query(dat , "GSE13015")
GSE13015 = res[["EH5429"]]
Group_df = Groupcomparison(GSE13015, sample_info = NULL,
                          FC = 0, pval = 0.1, FDR = TRUE, Test_group = "Sepsis",
                          Group_column = "Group_test", Ref_group = "Control")

[Package BloodGen3Module version 1.0.0 Index]