find_camera_hit: Find Camera Hit

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

Find Camera Hit

Description

This function implements the method by proposed by Wu and Smyth (2012). The original camera method is a gene set test, here is applied in the contest of a genetic screening and so it erforms a competitive barcode set test. The paper can be found here CAMERA

Usage

find_camera_hit(
  screenR_Object,
  matrix_model,
  contrast,
  number_barcode = 3,
  thresh = 1e-04,
  lfc = 1,
  direction = "Down"
)

Arguments

screenR_Object	The ScreenR object obtained using the create_screenr_object
matrix_model	The matrix that will be used to perform the linear model analysis created using model.matrix
contrast	A vector or a single value indicating the index or the name of the column the model_matrix with which perform the analysis
number_barcode	Number of barcode that as to be differentially expressed (DE)in order to consider the gene associated DE. Example a gene is associated with 10 shRNA we consider a gene DE if it has at least number_barcode = 5 shRNA DE.
thresh	The threshold for the False Discovery Rate (FDR) that has to be used to select the statistically significant hits.
lfc	The Log2FC threshold.
direction	String containing the direction of the variation, "Down" for the down regulation "Up" for the up regulation.

Value

The data frame containing the hit found using the camera method

Examples

object <- get0("object", envir = asNamespace("ScreenR"))

matrix <- model.matrix(~ slot(object, "groups"))
colnames(matrix) <- c("Control", "T1/T2", "Treated")

result <- find_camera_hit(
    screenR_Object = object,
    matrix_model = matrix, contrast = "Treated"
)
head(result)

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