SCRATsummary: SCRATsummary

In zji90/SCRAT: SCRAT: Single-Cell Regulome Analysis Tool

Description

Compile SCRAT summary table

Usage

SCRATsummary(dir = "", genome, bamfile = NULL, singlepair = "automated",
  removeblacklist = T, log2transform = T, featurelist = c("GENE", "ENCL",
  "MOTIF_TRANSFAC", "MOTIF_JASPAR", "GSEA"), Genestarttype = "TSSup",
  Geneendtype = "TSSdown", Genestartbp = 3000, Geneendbp = 1000,
  ENCLclunum = 2000, Motifflank = 100, GSEAterm = "c5.bp",
  GSEAstarttype = "TSSup", GSEAendtype = "TSSdown", GSEAstartbp = 3000,
  GSEAendbp = 1000)

Arguments

dir	The folder where the bam files are stored. If bamfile is NULL, all bam files within the folder will be analyzed.
genome	The mapped genome of the bam files. Should be one the following: "hg19", "hg38", "mm9", "mm10"
bamfile	A character vector of bam files. If NULL, all files in dir will be included.
singlepair	Whether the original sequencing files are single-end or paired-end. Should be one of the following: "automated", "single", "pair". Default is "automated" where SCRAT will automatically determine the type.
removeblacklist	Logical value indicating whether black list regions should be removed.
log2transform	Logical value indicating whether the read counts should be log2 transformed (after adding pseudo-count of 1).
featurelist	A character vector specifying what kind of features should be considered. Should be from the following: "GENE","ENCL","MOTIF_TRANSFAC","MOTIF_JASPAR","GSEA". By default all features are included. Note that "GSEA" features could be slow to run.
Genestarttype	For "GENE" features, type of starting site. Should be one of the following: "TSSup", "TSSdown", "TESup", "TESdown". The four options stands for TSS upstream, TSS downstream, TES upstream and TES downstream.
Geneendtype	For "GENE" features, type of ending site. Options same as Genestarttype
Genestartbp	For "GENE" features, how many base pairs away from starting TSS/TES. For example, Genestarttype="TSSup" and Genestartbp=500 means 500 bp upstream of TSS.
Geneendbp	For "GENE" features, how many base pairs away from ending TSS/TES.
ENCLclunum	Number of clusters for ENCL features. Should be one of 1000, 2000 and 5000
Motifflank	Defines the size of flanking region of motif sites in base pairs.
GSEAterm	The GSEA terms included in the analysis. Only useful when "GSEA" is included in featurelist. Should be one of the following: "h.all","c1.all","c2.cgp","c2.cp","c3.mir","c3.tft","c4.cgn","c4.cm","c5.bp","c5.cc","c5.mf","c6.all","c7.all".
GSEAstarttype	For "GSEA" features, type of starting site.
GSEAendtype	For "GSEA" features, type of ending site.
GSEAstartbp	For "GSEA" features, how many base pairs away from starting TSS/TES.
GSEAendbp	For "GSEA" features, how many base pairs away from ending TSS/TES.

Details

This function will compile a SCRAT summary table from bam files. The results should be the same as run on GUI.

Author(s)

Zhicheng Ji, Weiqiang Zhou, Hongkai Ji <[e-mail]>

Examples

## Not run: 
   SCRATsummary(dir="bamfiledir",genome="hg19")

## End(Not run)

zji90/SCRAT documentation built on April 7, 2020, 2:08 p.m.