computeCellLine: Compute Correlation between cell lines and vector of case...

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

Compute Correlation between cell lines and vector of case ids.

Description

Select top CCLE cell lines sharing similar expression profiles with input case samples. Input case sample ids and output correlation scores for every cell line and/or output file. The results could be used for in-silico validation of predictions or used to weight cell lines in RGES computation. CellLineCorrelations.csv, correlation between CCLE cell lines and input disease samples.

Usage

 computeCellLine(case_id = case_id, expSet = NULL, LINCS_overlaps = TRUE,
                            source = c("octad.small", "octad.whole", "expSet"),
                            file = NULL, output = TRUE,
                            outputFolder = NULL)

Arguments

case_id	vector of ids from octad database. Ids can be obtained from phenoDF.
output	by default FALSE, if TRUE, file CellLineCorrelations.csv with results are produced in working directory.
outputFolder	Folder to store results.
LINCS_overlaps	vector of cell line ids from octad database. If TRUE, overlap with LINCS cells database wll be performed
source	the file for the octad expression matrix. By default, set to octad.small to use only 978 landmark genes profiled in LINCS database. Use octad.whole option to compute DE on the whole transcriptome octad.counts.and.tpm.h5 file. The file should be present in the working directory or the whole path should be included. If source is set to 'side', the expSet matrix is estimated.
expSet	input expression matrix. By default set to NULL since the expSet is created based on cases, controls and source file.
file	if expSet='octad.whole', source path to expSet='octad.counts.and.tpm.h5' file is required if it is not in working directory. By default function seeks for the .h5 file in the working directory.

Value

topline

data.frame with row.names as cell line names and column medcor containing values for correlation between set of samples from case_id and cell lines.

See Also

runsRGES

Examples

#load data.frame with samples included in the OCTAD database
phenoDF=get_ExperimentHub_data('EH7274') 
HCC_primary=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&
sample.type == 'primary') #select data
case_id=HCC_primary$sample.id #select cases
cell_line_computed=computeCellLine(case_id=case_id,source='octad.small')

Bin-Chen-Lab/OCTAD documentation built on Jan. 28, 2023, 12:04 p.m.