OmicInt (version 1.1.7)

score_genes: score_genes

Description

Function collects data from STRINGDB and disease association databases to scale as well as prepare additional score integration. Function returns a data frame with calculated scores for downstream analyses.

Usage

score_genes(data, alpha = "association", beta = FALSE, gamma = FALSE)

Arguments

data

requires a path variable to CSV file containing gene names as row names and a column with LFC values in csv format (comma separated). Columns must contain values: 'Symbol', "log2FoldChange", and 'pvalue'. Class - data frame

alpha

default value returns "association" which gives a score from 0 to 1 based on how strongly the gene is associated with a disease or pathological phenotype; other options are "specificity" - to give values based on how specific the gene is for a given disease and "geometric" - to give a geometric score of both association and specificity. Class - string

beta

default FALSE; if TRUE, please supply data with column beta that contains information on gene associations from single cell studies. Class - string

gamma

default FALSE; if TRUE, please supply data with column gamma that contains information on gene associations from proteome studies. Class - string

Value

a data frame with calculated score values for the downstream analyses; class - data frame

Examples

# NOT RUN {
path_to_test_data<- system.file("extdata", "data.csv", package="OmicInt")
#basic usage of score_genes function
df<-score_genes(path_to_test_data)
head(df)
# }