| check_genes_missing_noDir {ssdGSA} | R Documentation |
Function to Check if Genes in Gene Sets Have Missing Information in Data Matrix
Description
This function is to check if genes in gene sets to be analyzed have missing information in data matrix.
Usage
check_genes_missing_noDir(Gene_sets, Data)
Arguments
Gene_sets |
A list of gene sets to be analyzed, with gene set names as component names, and each component is a vector of gene entrez ID. |
Data |
Data matrix of gene expressions with gene ensembl ID as row names and columns corresponding to different samples. |
Details
Before single sample directional gene set analysis, it is necessary to check if genes in the gene sets have missing information in data matrix. If not, warning messages would be given such that users can double check whether the gene set analysis results are reliable.
Value
When at least one gene in the gene sets have information missing in data matrix, warning messages will be given, as well as the percentages (missing number/total number) of gene sets. If less than 10 gene sets have missing information, percentages (missing number/total number) of genes in each gene set that have missing information in data matrix and direction matrix will also be reported. However, if more than 10 gene sets have missing information, no detailed individual gene set missing information will be reported. Also note that if a gene set has 100% information missing in the data matrix, the name of the gene set will be notated.