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ssdGSA (version 0.1.1)

Single Sample Directional Gene Set Analysis

Description

A method that inherits the standard gene set variation analysis (GSVA) method and also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. Note to use this package, GSVA(>= 1.52.1) is needed to pre-installed. Hanzelmann, S., Castelo, R., and Guinney, J. (2013) .

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Version

Install

install.packages('ssdGSA')

Monthly Downloads

140

Version

0.1.1

License

GPL-2

Maintainer

Xingpeng Li

Last Published

July 26th, 2024

Functions in ssdGSA (0.1.1)

data_matrix

This is data to be included in package
check_gene_name_match_noDir

Function to Check if Gene IDs in the Input Gene Data Match Well When Direction Matrix Is Missing
check_genes_missing_total

Function to Check if 100% of Genes in Gene Sets Have Missing Information in Data Matrix
check_genes_missing_noDir

Function to Check if Genes in Gene Sets Have Missing Information in Data Matrix
avg_expression

Function to Calculate the Average of Gene Expressions
check_genes_missing

Function to Check if Genes in Gene Sets Have Missing Information in Data Matrix and Direction Matrix
check_gene_name_match

Function to Check if Gene IDs in the Input Gene Data Match Well
transform_ensembl_2_entrez

Function to Transform ENSEMBL ID to ENTREZ ID
median_expression

Function to Calculate Median of Gene Expressions
direction_matrix

This is data to be included in package
gene_sets

This is data to be included in package
data_matrix_entrezID

This is data to be included in package
ssdGSA

Single Sample Directional Gene Set Analysis (ssdGSA)
ssGSA

Function to Calculate Single Sample Gene Set Scores without Direction Matrix
ssdGSA_individual

Single Sample Directional Gene Set Analysis Using Individual Weighted Scores