gene_stat: General stastitics of ImSig analysis

In imsig: Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours

Description

[Total genes in ImSig]: The total number of genes in ImSig list. [No. of ImSig genes in user dataset]: The number of ImSig genes found in user's dataset. Like all signatures, ImSig works best when this overlap is high, preferably over 75

Usage

gene_stat(exp, r = 0.6)

Arguments

exp

Dataframe of transcriptomic data (natural scale) containing genes as rows and samples as columns. Note: Gene names should be set as row names and duplicates are not allowed. Missing values are not allowed within the expression matrix. Check example- head(example_data): example_data.

r

Use a value between 0 and 1. Default is 0.6. This is a user defined correlation cut-off to perform feature selection (feature_select). Feature selection aids to enrich the prediction of relative abundance of immune cells by filtering off poorly correlated ImSig genes. To get an idea of what cut-off to use check the results of (gene_stat) and choose a cut-off that displays high median correlation and maintains a high proportion of genes after feature selection.

Value

Dataframe of general statistics of ImSig analysis.

See Also

feature_select

Examples

gene_stat (exp = example_data, r = 0.7)

imsig documentation built on Jan. 13, 2021, 9:51 p.m.