findIT_MARA: findIT_MARA

In shangguandong1996/FindIT2: find influential TF and Target based on multi-omics data

findIT_MARA

Description

findIT_MARA

Usage

findIT_MARA(
  input_feature_id,
  peak_GR,
  peakScoreMt,
  TF_GR_database,
  log = TRUE,
  meanScale = TRUE,
  output = c("coef", "cor"),
  verbose = TRUE
)

Arguments

input_feature_id	a character vector which represent peaks set which you want to find influential TF for
peak_GR	a GRange object represent your whole feature location with a column named feature_id, which your input_feature_id should a part of it.
peakScoreMt	peak count matrix.
TF_GR_database	TF peak GRange with a column named TF_id representing you TF name. If you have TF_score column, MARA will consider it. otherwise, MARA will consider each hit is 1.
log	whether you want to log your peakScoreMt
meanScale	whether you want to mean-centered per row
output	one of 'coef' and 'cor'. Default is coef
verbose	whether you want to report detailed running message

Value

a data.frame

Examples

data("ATAC_normCount")
data("test_featureSet")

peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2")
peak_GR <- loadPeakFile(peak_path)

ChIP_peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2")
ChIP_peak_GR <- loadPeakFile(ChIP_peak_path)
ChIP_peak_GR$TF_id <- "AT1G28300"

set.seed(20160806)

result_findIT_MARA <- findIT_MARA(
    input_feature_id = test_featureSet,
    peak_GR = peak_GR,
    peakScoreMt = ATAC_normCount,
    TF_GR_database = ChIP_peak_GR
)

shangguandong1996/FindIT2 documentation built on March 1, 2024, 8:34 p.m.