Man pages for rosedu1/deconvSeq
Cell Type Deconvolution for RNA Sequencing and Bisulfite Sequencing

cbc.rnaseqKnown cell type mixture for tissue (RNAseq)
cbc.rrbsKnown cell type mixture for tissue (bisulfite sequencing)
celltypes.rrbsvector of kinds of cell types (bisulfite sequencing)
cnts.celltypesCount matrix for cell types (RNAseq)
cnts.scCount matrix for single cell RNAseq after filtering for count...
cnts.sc.G1Count matrix for single cell RNAseq after filtering cnts.sc...
cnts.scrnaseqCount matrix for single cell RNAseq (scRNAseq)
cnts.tissueCount matrix for tissue (RNAseq)
data_celltypes_rnaseqThis is the example cell type data for RNA sequencing
data_celltypes_rrbsThis is the example cell type data for bisulfite sequencing
data_scrnaseqThis is the example data for scRNA sequencing
data_tissue_rnaseqThis is the example tissue data for RNA sequencing
data_tissue_rrbsThis is the example tissue data for bisulfite sequencing
design.rnaseqDesign matrix for cell types (RNAseq)
design.rrbsDesign matrix for cell types (bisulfite sequencing)
dge.celltypesDGE object (from EdgeR) of RNAseq results for cell types
dge.tissueDGE object (from EdgeR) of RNAseq results for tissue
getb0.biseqcompute b0, projection matrix, given methylation counts
getb0.rnaseqcompute b0, projection matrix, given counts
getcellcyclefilter for cells with particular cell cycle phase: "G1",...
getcorrcompute correlation between estimated and actual composition...
getdgeobtain EdgeR DGE object from count matrix
getmeancorrget mean correlation by first doing Fisher transform to z,...
getmethmatmakes methylation count matrix using output from BSMAP....
getrnamattakes count matrix for individual samples (e.g. output of...
getx1.biseqcompute mixture data given projection matrix (bisulfite...
getx1.rnaseqcompute mixture data given projection matrix (RNAseq)
methmatmethylation matrix for cell types (bisulfite sequencing)
methmat.tissuemethylation matrix for tissue (bisulfite sequencing)
my_diffMethFromDesign_matrixmodified from methylKit, performs regression given...
prep_scrnaseqdo quality control of scRNAseq based on library size, feature...
sample.id.rnaseqSample IDs for cell types (RNAseq)
sample.id.rrbsSample IDs for cell types (bisulfite sequencing)
sample.id.tissueSample IDs for tissue (bisulfite sequencing)
rosedu1/deconvSeq documentation built on May 24, 2019, 8:52 a.m.