importScSeqScore {trackViewer} | R Documentation |
Plot single cell RNAseq data as heatmap track for Seurat object.
importScSeqScore( object, files, samplenames, ..., txdb, gene, id, idents, gr, color, withCoverageTrack = TRUE, flag = scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery = FALSE, isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE) )
object |
Seurat object. |
files |
bam file to be scanned. |
samplenames |
sample names for files. |
... |
parameters used by readGAlignmentsList or readGAlignments |
txdb |
TxDb object for gene model. |
gene |
Gene name to plot. (row value) |
id |
The id of gene used in txdb. |
idents |
indentity class to define the groups to plot. (column value) |
gr |
GRanges object to define the ploting region. |
color |
vector of colors used in heatmap. |
withCoverageTrack |
plot coverage track or not. |
flag |
An integer(2) vector used to filter reads based on their 'flag' entry. |
## Not run: library(TxDb.Hsapiens.UCSC.hg19.knownGene) test_file <- "https://github.com/10XGenomics/subset-bam/raw/master/test/test.bam" trs <- importScSeqScore(files=test_file, txdb=TxDb.Hsapiens.UCSC.hg19.knownGene, id="653635", gene = "WASH7P") ## End(Not run)