jaccard_findIT_enrichFisher: jaccard_findIT_enrichFisher

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

jaccard_findIT_enrichFisher

Description

jaccard_findIT_enrichFisher

Usage

jaccard_findIT_enrichFisher(
  input_feature_id,
  peak_GR,
  TF_GR_database,
  input_TF_id
)

Arguments

input_feature_id	a character vector which represent peaks set which you want to find influential TF for (same as your find_IT_enrichFisher parameter)
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.
TF_GR_database	TF peak GRange with a column named TF_id representing you TF name
input_TF_id	TF_id which you want to calculate jaccard index for

Value

jaccard similarity matrix

Examples

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"
result_findIT_enrichFisher <- findIT_enrichFisher(
    input_feature_id = test_featureSet,
    peak_GR = peak_GR,
    TF_GR_database = ChIP_peak_GR
)

jaccard_findIT_enrichFisher(
    input_feature_id = test_featureSet,
    peak_GR = peak_GR,
    TF_GR_database = ChIP_peak_GR,
    input_TF_id = result_findIT_enrichFisher$TF_id[1]
)

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