filter_original_regulation | R Documentation |
This function is used to further filter regulation generated by Genin3, PIDC, or other methods.
filter_original_regulation(
potential_regulation,
motif,
tf_threshold = 500,
target_threshold = 100
)
potential_regulation |
data.frame consists of three columns, first column contains source genes, second column contains target genes, third column contains weight. |
motif |
motif file, you can choose our bulit-in motif database of 'mus musculus', 'homo sapiens', 'zebrafish' and 'chicken' by 'motif = Tranfac201803_Mm_MotifTFsF', 'motif = Tranfac201803_Hs_MotifTFsF', 'motif = Tranfac201803_Zf_MotifTFsF', 'motif = Tranfac201803_Ch_MotifTFsF' respectively, or you can upload your own motif data base, but the formata use be the same as our built-in motif database. |
tf_threshold |
the numbers of targets with highest weight of each transcription factor. Indicating the threshold to filter regulation. |
target_threshold |
numbers of top transcription factors for each target. Indicating the threshold to filter regulation. |
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