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

Description Usage Arguments Value See Also Examples

View source: R/computeCellLine.R

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

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 computeCellLine(case_id =case_id,expSet=NULL,LINCS_overlaps = TRUE,source='octad.small',file=NULL,returnDF = FALSE)

Arguments

case_id

vector of ids from octad database. Ids can be obtained from phenoDF.

returnDF

by default FALSE, if TRUE, file CellLineCorrelations.csv with results are produced in working directory.

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

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 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,returnDF=TRUE)
 computeCellLine(case_id,returnDF=TRUE,source='octad.small')

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