processInput: processInput

In dkornai/QuieScore: Uses Single Cell Gene Expression Data to Score Tumor Quiescence

processInput

Description

This function takes user supplied data frames of gene expression data, and formats them to be suitable for the 'QuiescenceScore' function

Usage

processInput(input_object, cancer_type, gene_naming, log_transformed = TRUE)

Arguments

input_object	dataframe containing gene expression data, columns are samples, rows are genes
cancer_type	the 3 or 4 letter code of the cancer type in the submitted samples. Can only be 1 type.
gene_naming	which type of naming scheme are used to specify the genes? set to 'name' for names, and 'ensg' for ENSG
log_transformed	Optional Parameter, the default value is TRUE. If the expression data needs to get log2 transformed, manually specify FALSE

Value

A list formatted object that can be passed to the "QuiescenceScore" function

Examples

patient1_data_processed <- processInput(patient1_data_raw, cancer_type = "LUAD", gene_naming = "name")
patient2_data_processed <- processInput(patient2_data_raw, cancer_type = "BRCA", gene_naming = "ensg")
patient3_data_processed <- processInput(patient3_data_raw, cancer_type = "PAAD", gene_naming = "ensg", log_transformed = FALSE)

dkornai/QuieScore documentation built on July 3, 2024, 2:29 p.m.