View source: R/findIT_TTpair_enrichFisher_parse.R
jaccard_findIT_enrichFisher | R Documentation |
jaccard_findIT_enrichFisher
jaccard_findIT_enrichFisher(
input_feature_id,
peak_GR,
TF_GR_database,
input_TF_id
)
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 |
jaccard similarity matrix
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]
)
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