find2Kat

Description

Find2Kat this package, can implement calleak and annote bam, bed file, but also can implement the ArchR object DORC score calculation (generally only on the share-seq data), as well as can achieve the correlation between cell type and disease and so on(Many object inputs based on ArchR Object) ...

installtation

install.packages("find2Kat_0.2.0.tar.gz")

you also need to install depend packages via dependency

callpeak for BAM or BED file and annotation

you can use function annoteFile reliaze

annoteFile(File="yourPathOfFiles",Names="relativeNames",blacklist=find2Kat::blacklist[["hg38"]],genome="hg38",...)

and the result like follow

ChipSeeker Annotation after MACS2 CallPeak

summitsChipSeekerAnnote(...)
chipseekerGO(..) # GO pathway analysis

DOCR Score

getDORCXMatrix function can get DORC score(it will take many minutes...);and DOCRPointPlot can show DORC Rank gene scatter plot reliaze it via code

dorcList=getDORCXMatrix(projHeme)
x=dorcList[["CellTypeDORC"]]
colData=data.frame("Clusters"=colnames(x))
ArchRHeatmap(mat=as.matrix(x),colData=colData,showRowDendrogram=TRUE,scale=TRUE,customRowLabel =c(1,3,5,7))

reliaze it via code

DOCRPointPlot(p2g,genes=genes,nShowGenes=10,..)

detail can refer to function help

celltype to Disease

how to related CellType to Disease

chromVARSNPpipeline(...)

Link to TF

data("GeneGTF")
getP2GLinks(...)
link2TF(...)

Motif Module for Granges Object

#features Granges Object,eg,getPeakSet(ArchRProject)
data("pwms")
motif.obj<-GRangesAddMotifs(object=features,genome=BSgenome.Mmusculus.UCSC.mm10,pfm=pwms[["mouse"]])
MotifPlot(motif.obj,motifs=c(..),..)

get Count from BAM file after aligment of fastq files

se=bam2Count(bamfiles=bamFiles,bamNames=bamNames,peaks=peaks)

PS : you can get gtf gene GRanges object with gene.gtf by code getGeneGTF.R

Issues using yipCat?

If this does not fix your problem, please report an issue on Github with the Bug Report form.