filter_by_variance: Filter using the variance filter

In EmanuelSoda/ScreenR: Package to Perform High Throughput Biological Screening

Filter using the variance filter

Description

This function is used to improve the quality of the hits. It compute the variance among the hits and filter the one with a value greater than the threshold set

Usage

filter_by_variance(
  screenR_Object,
  genes,
  matrix_model,
  variance = 0.5,
  contrast
)

Arguments

screenR_Object	The ScreenR object obtained using the create_screenr_object
genes	The genes for which the variance as to be computed. Those genes are the result of the three statistical methods selection
matrix_model	a matrix created using model.matrix
variance	The maximum value of variance accepted
contrast	The variable to use as X for the linear model for the Treatment

Value

A data frame with the variance for the treatment and the control for each gene

Examples

object <- get0("object", envir = asNamespace("ScreenR"))
matrix_model <- model.matrix(~ slot(object, "groups"))
colnames(matrix_model) <- c("Control", "T1_T2", "Treated")
contrast <- limma::makeContrasts(Treated - Control, levels = matrix_model)

data <- filter_by_variance(
    screenR_Object = object, genes = c("Gene_42"),
    matrix_model = matrix_model, contrast = contrast
)
head(data)

EmanuelSoda/ScreenR documentation built on Sept. 29, 2023, 12:33 a.m.