extdata: Data in extdata

In jianhong/ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq

Data in extdata

Description

The list of data saved in extdata folder.

Details

The 'PWMatrixList' is a collection of jasper2018, jolma2013 and cisbp_1.02 from package motifDB (v 1.28.0) and merged by distance smaller than 1e-9 calculated by MotIV::motifDistances function (v 1.42.0). The merged motifs were exported by motifStack (v 1.30.0).

The 'cluster_PWMs' is a list of non-redundant TF motifs downloaded from [DeepSTARR](https://github.com/bernardo-de-almeida/motif-clustering). There are 6502 motifs in the data set.

The 'best_curated_Human' is a list of TF motifs downloaded from [TFEA github](https://github.com/Dowell-Lab/TFEA). There are 1279 human motifs in the data set.

Examples

motifs <- readRDS(system.file("extdata", "PWMatrixList.rds",
                  package="ATACseqTFEA"))
motifs2 <- readRDS(system.file("extdata", "cluster_PWMs.rds",
                   package="ATACseqTFEA"))
motifs3 <- readRDS(system.file("extdata", "best_curated_Human.rds",
                   package="ATACseqTFEA"))

jianhong/ATACseqTFEA documentation built on Feb. 9, 2024, 4:09 a.m.