Description Usage Arguments Value Examples
Count unique UMI:gene pairs for single cell RNA-sequencing alignment
files. Write resulting count matrix to output directory. Columns are
samples (cells) and rows are gene IDs. The input sequence alignment files
must be generated using FASTQ files generated by the demultiplex
function in scruff package. Return a SingleCellExperiment object containing
the count matrix, cell and gene annotations, and all QC metrics.
1 2 3 4 |
sce |
A |
reference |
Path to the reference GTF file. The TxDb object of the GTF file will be generated and saved in the current working directory with ".sqlite" suffix. |
umiEdit |
Maximally allowed Hamming distance for UMI correction. For
read alignments in each gene, by comparing to a more abundant UMI with more
reads, UMIs having fewer reads and with mismatches equal or fewer than
|
format |
Format of input sequence alignment files. "BAM" or "SAM". Default is "BAM". |
outDir |
Output directory for UMI counting results. UMI corrected count
matrix will be stored in this directory. Default is |
cellPerWell |
Number of cells per well. Can be an integer (e.g. 1) indicating the number of cells in each well or an vector with length equal to the total number of cells in the input alignment files specifying the number of cells in each file. Default is 1. |
cores |
Number of cores used for parallelization. Default is
|
outputPrefix |
Prefix for expression table filename. Default is
|
verbose |
Print log messages. Useful for debugging. Default to FALSE. |
logfilePrefix |
Prefix for log file. Default is current date and time
in the format of |
A SingleCellExperiment object.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | ## Not run:
data(barcodeExample, package = "scruff")
# The SingleCellExperiment object returned by alignRsubread function and the
# alignment BAM files are required for running countUMI function
# First demultiplex example FASTQ files
fastqs <- list.files(system.file("extdata", package = "scruff"),
pattern = "\\.fastq\\.gz", full.names = TRUE)
de <- demultiplex(
project = "example",
experiment = c("1h1", "b1"),
lane = c("L001", "L001"),
read1Path = c(fastqs[1], fastqs[3]),
read2Path = c(fastqs[2], fastqs[4]),
barcodeExample,
bcStart = 1,
bcStop = 8,
umiStart = 9,
umiStop = 12,
keep = 75,
overwrite = TRUE)
# Alignment
library(Rsubread)
# Create index files for GRCm38_MT.
fasta <- system.file("extdata", "GRCm38_MT.fa", package = "scruff")
# Specify the basename for Rsubread index
indexBase <- "GRCm38_MT"
buildindex(basename = indexBase, reference = fasta, indexSplit = FALSE)
al <- alignRsubread(de, indexBase, overwrite = TRUE)
# Counting
gtf <- system.file("extdata", "GRCm38_MT.gtf", package = "scruff")
sce = countUMI(al, gtf, cellPerWell=c(rep(1, 94), 0, 0, rep(1, 94), 300, 1))
## End(Not run)
# or use the built-in SingleCellExperiment object generated using
# example dataset (see ?sceExample)
data(sceExample, package = "scruff")
|
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