find_roast_hit: Find Roast Hit

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

Find Roast Hit

Description

Find the hit using the roast method. Roast is a competitive gene set test which uses rotation instead of permutation. Here is applied in a contest of a genetic screening so it perform a barcode competitive test testing for barcode which are differentially expressed within a gene. More information can be found in Roast

Usage

find_roast_hit(
  screenR_Object,
  matrix_model,
  contrast,
  nrot = 9999,
  number_barcode = 3,
  direction = "Down",
  p_val = 0.05
)

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 to which perform the analysis
nrot	Number of rotation to perform the test. Higher number of rotation leads to more statistically significant result.
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.
direction	Direction of variation
p_val	The value that as to be used as p-value cut off

Value

The hits found by ROAST method

Examples

set.seed(42)
object <- get0("object", envir = asNamespace("ScreenR"))
matrix_model <- model.matrix(~ slot(object, "groups"))
colnames(matrix_model) <- c("Control", "T1_T2", "Treated")

result <- find_roast_hit(object,
    matrix_model = matrix_model,
    contrast = "Treated", nrot = 100
)
head(result)

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