runsRGES: Compute sRGES

In Bin-Chen-Lab/octad_desktop: Open Cancer TherApeutic Discovery (OCTAD)

Description

Compute sRGES, a score indicating the reveral potency of each drug. It first computes RGES (Reverse Gene Expression Score) for individual instances and then summarizes RGES of invididual drugs (one drug may have multiple instances under different treatment conditions).

Usage

 runsRGES(dz_signature=NULL,choose_fda_drugs = FALSE,max_gene_size=500, 
                     cells=NULL,outputFolder=NULL,weight_cell_line=NULL,permutations=10000)

Arguments

dz_signature	disease signature. Make sure input data frame has a gene Symbol column, otherwise an error is produced. It must be an UPPERCASE gene symbol.
choose_fda_drugs	if TRUE, only FDA approved drugs are used.
max_gene_size	maximum number of disease genes used for drug prediction. By default 50 for each side (up/down).
cells	cell ids in lincs_sig_info file used for prediction. By default, all cell lines are used.
outputFolder	folder path to store drug results, by default write results to working directory.
weight_cell_line	by default NULL, if !NULL, an output object from computeCellLine is estimated (see example).
permutations	number of permutations, by default 10000.

Value

The function returns RGES data.frame

containing scores and p.values for every instance. data.frame contains drug id in pert_iname collumn, n contains the number of instances for this drug, mean, median and sd of sRGES RGES sores.

Besides, a number of additional files in the sourced directory:

dz_sig_used.csv	contains genes in the disease signature used for computing reverse gene expression scores.
sRGES.csv	contains the same data as returned data.frame.
all__lincs_score.csv	includes information of RGES.

See Also

diffExp, octadDrugEnrichment, computeCellLine, topLineEval

Examples

HCC_primary=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&sample.type == 'primary') #select data
case_id=HCC_primary$sample.id #select cases
HCC_adjacent=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&sample.type == 'adjacent'&data.source == 'TCGA') #select data
control_id=HCC_adjacent$sample.id #select cases
res=diffExp(case_id,control_id,source='octad.small',output=TRUE)
res=subset(res,abs(log2FoldChange)>2)
#run sRGES computation
runsRGES(dz_signature=res)

Bin-Chen-Lab/octad_desktop documentation built on Oct. 28, 2020, 11:13 a.m.