computeRefTissue: Compute correlating reference control samples.

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

Compute correlating reference control samples.

Description

Compute reference control samples from OCTAD database using precomputed EncoderDF models.

Usage

 computeRefTissue(case_id = NULL, adjacent = FALSE, source = "octad",
 n_varGenes = 500, method = c("varGenes",'random'), expSet = NULL,
control_size = length(case_id),
outputFolder = NULL, cor_cutoff = "0", output = TRUE)

Arguments

case_id	vector of cases used to compute references.
source	by default set octad to use autoencoder results for computation. Any other input like 'side' is expSet defined by users.
adjacent	by default set to FALSE. If TRUE, only tissue with sample.type 'adjacent' from phenoDF would be used instead of 'normal'.
expSet	input for expression matrix. By default NULL, since autoencoder results are used.
n_varGenes	number of genes used to select control cases.
method	one of two options is avaliable. random will take a random number of samples from control subset and varGenes (default) will select control samples based on distance between cases and selected samples.
control_size	number of control samples to be selected.
outputFolder	path to output folder. By default, the function produces result files in working directory.
cor_cutoff	cut-off for correlation values, by default cor_cutoff='0'.
output	if TRUE, two output files are produced.

Value

Return

control_id

a vector of an appropriate set of control samples.

Besides, if output=TRUE, two files are created in the working directory:

case_normal_corMatrix.csv	contains pairwise correlation between case samples vs control samples.
case_normal_median_cor.csv	contains median correlation values with case samples for returned control samples.

See Also

diffExp.

Examples

#select data
#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'&data.source == 'TCGA')
#select cases
case_id=HCC_primary$sample.id
#computing reference tissue, by default using small autoEncoder,
#but can use custom expression set,
#by default output=TRUE and outputFolder option is empty,
#which creates control corMatrix.csv to working directory
control_id=computeRefTissue(case_id,outputFolder='',output=TRUE,
expSet = "octad",control_size = 50)

Bin-Chen-Lab/octad documentation built on Jan. 28, 2023, 11:20 p.m.