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Find Camera Hit

Source: R/camera_method.R
find_camera_hit.Rd

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"
)
#> Warning: 3rows with all zero counts
#> Warning: Zero sample variances detected, have been offset away from zero
head(result)
#> # A tibble: 6 × 5
#>   Gene     NGenes Direction    PValue    FDR
#>   <chr>     <dbl> <fct>         <dbl>  <dbl>
#> 1 Gene_173     10 Down      0.0000286 0.0153
#> 2 Gene_15      10 Down      0.00371   0.372 
#> 3 Gene_352     10 Down      0.00779   0.485 
#> 4 Gene_121     10 Down      0.0111    0.533 
#> 5 Gene_422     10 Down      0.0128    0.533 
#> 6 Gene_377     10 Down      0.0129    0.533