imogimap: imogimap: Immuno-oncology gene expression assessment.

In korkutlab/imogimap: What the Package Does (One Line, Title Case)

imogimap: Immuno-oncology gene expression assessment.

Description

The imogimap package provides three categories of functions:

Functions to use public TCGA data

The following functions use curatedTCGAData to obtain publicly available RNASeq2GeneNorm data from The Cancer Genome Atlas (TCGA).

• im_syng_tcga: Finds combinatorial association of immunotherapy co-targets with tumor intrinsic features as listed in TCGA_immune_features_list.

• im_boxplot_tcga: Generates a stratified boxplot of immune feature values based on two genes

• im_cor_tcga: Finds Spearman correlation of co-target genes with immuno-oncology feature

Functions to use with user-curated data

The following functions accept user-curated expression data as input.

• im_syng: Finds combinatorial association of immunotherapy co-targets with tumor intrinsic features as listed in TCGA_immune_features_list.

• im_boxplot: Generates a stratified boxplot of immune feature values based on two genes

• im_cor: Finds Spearman correlation of co-target genes with immuno-oncology feature

Functions for output visualization and helper functions

• im_netplot: Creates and plot an igraph network from dataframe as outputed

• find_a_synergy: Evalues synergies for a data frame containing values of an immune feature and stratified expression levels of two genes.

• calculate_syng_score: Calculates a synergy score given median and standard error of means of four stratified groups

• get_angio_score: Calculates angiogenesis score

• get_emt_score: Calculates EMT score

• get_ifng_score: Calculates IFNG score

• get_quantile_rank: Stratify each column using quantile values.

Sample data sets and gene signature lists

• AG_gene_list: Angiogenesis signature genes

• EMT_gene_list: EMT signature genes

• icp_gene_list: Default list of immune checkpoints

• sample_immune_cell_fraction_data: Sample immune cell fraction data

• sample_Leukocyte_fraction_data: Sample Leukocyte fraction data

• sample_mRNA_data: Sample expression data

• TCGA_Leukocyte_fraction: Leukocyte fraction for TCGA data

• TCGA_IMCell_fraction: Immune cell type fractions for TCGA data

• TCGA_TMB: Tumor mutation burden for TCGA data

• TCGA_immune_features_list: Default immune features for TCGA data

• TCGA_disease_list: TCGA abbreviated disease names

korkutlab/imogimap documentation built on March 17, 2023, 8:22 a.m.