Align Single Cell RNA-Seq Data and Create a SCtkExperiment Object

alignSingleCellData(inputfile1, inputfile2 = NULL, indexPath,
  gtfAnnotation, outputDir = NULL, sampleAnnotations = NULL,
  featureAnnotations = NULL, threads = 1, saveBam = FALSE,
  saveCountFiles = FALSE, isPairedEnd = FALSE)

Arguments

inputfile1

An input file or list of files. Files can be fastq, fastq.gz, or bam, but must all be of the same type. Sample names will be the full file name, without _1.fastq.gz, .fastq.gz, _1.fastq, .fastq or .bam endings.

inputfile2

If fastq files are provided in input list, a list of corresponding paired fastq files, if applicable.

indexPath

Path to the Rsubread genome index.

gtfAnnotation

Path to the GTF gene annotation to use. This must correspond to the genome specified in indexPath.

outputDir

If saveBam or saveCountFiles is TRUE, specify a directory in which to save the output files.

sampleAnnotations

A data.frame of sample annotations, with samples as rows and annotations in columns. The sample names must be identical to and in the same order as the list of files in inputfile1. Alignment statistics will be added to the annotation data frame.

featureAnnotations

An optional data.frame of probe annotations, with probes as rows and probe annotations in columns.

threads

Number of threads to use during alignment. The default is 1.

saveBam

If TRUE, bam alignment files will be saved in the outputDir. The default is FALSE.

saveCountFiles

If TRUE, per sample gene count files will be saved in the outputDir. The default is FALSE.

isPairedEnd

If input files are .bam, indicate whether the input bam files are paired end.

Value

Object to import into the shiny app.

Examples

# NOT RUN {
singlecellobject <- alignSingleCellData(
  inputfile1 = c("/path/to/sample1_1.fastq.gz",
                 "/path/to/sample2_1.fastq.gz"),
  inputfile2 = c("/path/to/sample1_2.fastq.gz",
                 "/path/to/sample2_2.fastq.gz"),
  indexPath = "/path/to/genome/index",
  gtfAnnotation = "/path/to/gene/annotations.gtf",
  sampleAnnotations = sample.annotation.df,
  threads=4)
# }