Groupcomparison: Group comparison analysis

In Drinchai/BloodGen3Module: This R package for performing module repertoire analyses and generating fingerprint representations

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.

• Expression matrix and sample annotation files are required to perform this analysis.

• The sample annotation file must be loaded using a specific name = "sample_info".

• The names of the columns for the conditions used in the analysis must be specified.

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 [e-mail]

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")

Drinchai/BloodGen3Module documentation built on Sept. 20, 2021, 10:31 p.m.