computeCellLine: Compute Correlation between cell lines and vector of case...
In Bin-Chen-Lab/octad_desktop: Open Cancer TherApeutic Discovery (OCTAD)

Description Usage Arguments Value See Also Examples

View source: R/computeCellLine.R

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.

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

`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.

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.

runsRGES

 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')