Description Usage Arguments Details Value Author(s) Examples
Preprocessing scATAC-seq samples
1 | satacprocess(input, type = "bam", libsizefilter = 1000)
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input |
Either a character vector of locations to bam files (when type is bam) or list of GRanges object of scATAC-seq reads (when type is gr). |
type |
Either 'bam' or 'gr'. 'bam' if the input is locations to bam files. 'gr' if the input is a list of GRanges object. |
libsizefilter |
Numeric variable giving the minimum library size. scATAC-seq samples with library size smaller than this cutoff will be discarded. |
This function filters out scATAC-seq with low library size and transforms the reads into middle points of the reads.
GRanges object of list of GRanges object after preprocessing.
Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji* <whou10@jhu.edu>
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