Conduct a differential test between open regions of two sample groups
Source:R/getDifferentialAccessibleTiles.R
getDifferentialAccessibleTiles.Rd
getDifferentialAccessibleTiles
allows you to
determine whether regions of chromatin are differentially accessible
between groups by conducting a test
Usage
getDifferentialAccessibleTiles(
SampleTileObj,
cellPopulation,
groupColumn,
foreground,
background,
signalThreshold = 12,
minZeroDiff = 0.5,
fdrToDisplay = 0.2,
outputGRanges = TRUE,
numCores = 1,
verbose = FALSE
)
Arguments
- SampleTileObj
The SummarizedExperiment object output from getSampleTileMatrix
- cellPopulation
A string denoting the cell population of interest
- groupColumn
The column containing sample group labels
- foreground
The foreground group of samples for differential comparison
- background
The background group of samples for differential comparison
- signalThreshold
Minimum median intensity required to keep tiles for differential testing to increase statistical power in small sample cohorts. Default is 12.
- minZeroDiff
Minimum difference in average dropout rates across groups require to keep tiles for differential testing. Default is 0.5 (50%).
- fdrToDisplay
False-discovery rate used only for standard output messaging. Default is 0.2.
- outputGRanges
Outputs a GRanges if TRUE and a data.frame if FALSE. Default is TRUE.
- numCores
The number of cores to use with multiprocessing. Default is 1.
- verbose
Set TRUE to display additional messages. Default is FALSE.
Value
full_results The differential accessibility results as a GRanges or matrix data.frame depending on the flag `outputGRanges`.
Examples
if (FALSE) {
cellPopulation <- "MAIT"
foreground <- "Positive"
background <- "Negative"
# Standard output will display the number of tiles found below a false-discovery rate threshold.
# This parameter does not filter results and only affects the aforementioned message.
fdrToDisplay <- 0.2
# Choose to output a GRanges or data.frame.
# Default is TRUE
outputGRanges <- TRUE
# SampleTileMatrices is the output of MOCHA::getSampleTileMatrix
differentials <- MOCHA::getDifferentialAccessibleTiles(
SampleTileObj = SampleTileMatrices,
cellPopulation = cellPopulation,
groupColumn = groupColumn,
foreground = foreground,
background = background,
fdrToDisplay = fdrToDisplay,
outputGRanges = outputGRanges,
numCores = numCores
)
}