tenxBamqc {scruff} | R Documentation

## Generate and output 10X read alignment data quality metrics

### Description

Read BAM file generated by Cell Ranger pipeline and output QC metrics including number of aligned reads and reads aligned to an gene.

### Usage

    tenxBamqc(
      bam,
      experiment,
      filter,
      validCb = NA,
      tags = c("NH", "GX", "CB", "MM"),
      yieldSize = 1e+06,
      outDir = "./",
      cores = max(1, parallel::detectCores() - 2)
    )

### Arguments

`bam` | Paths to input BAM files generated by Cell Ranger pipeline. These files are usually named "possorted_genome_bam.bam" in the "outs" folder of the top-level project output folders, respectively.
`experiment` | A character vector of experiment names. Represents the group label for each BAM file, e.g. "patient1, patient2, ...". The length of `experiment` equals the number of BAM files to be processed.
`filter` | Paths to the filtered barcode files. Should be in the same length and order of the input BAM files. These files are named "barcodes.tsv" located at outs/filtered_gene_bc_matrices/<reference_genome>/barcodes.tsv.
`validCb` | Path to the cell barcode whitelist file. By default uses the file "737K-august-2016.txt" which is compatible with the v2 chemistry protocol. The file can be inspected by calling `data(validCb, package = "scruff")`. If the library is generated using the v1 chemistry protocol, the path to the v1 barcode whitelist file ("737K-april-2014_rc.txt") needs to be provided. For library generated by v3 chemistry protocol, path to "3M-february-2018.txt" is needed.
`tags` | BAM tags used for collecting QC metrics. Contains non-standard tags locally-defined by Cell Ranger pipeline. Should not be changed in most cases.
`yieldSize` | The number of records (alignments) to yield when drawing successive subsets from a BAM file, providing the number of successive records to be returned on each yield. This parameter is passed to the `yieldSize` argument of the `BamFile` function in `Rsamtools` package. Default is 1e06.
`outDir` | Output directory. The location to write resulting QC table.
`cores` | Number of cores used for parallelization. Default is `max(1, parallel::detectCores() - 2)`, i.e. the number of available cores minus 2.

### Value

A SingleCellExperiment object. The `colData` contains the number of aligned reads (reads_mapped_to_genome) and reads aligned to genes (reads_mapped_to_genes).

### Examples

    # first 5000 records in the bam file downloaded from here:
    # http://sra-download.ncbi.nlm.nih.gov/srapub_files/
    # SRR5167880_E18_20160930_Neurons_Sample_01.bam
    # see details here:
    # https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP096558
    # and here:
    # https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93421
    bamfile10x <- system.file("extdata",
        "SRR5167880_E18_20160930_Neurons_Sample_01_5000.bam",
        package = "scruff")

    # library(TENxBrainData)
    # library(data.table)
    # tenx <- TENxBrainData()
    # # get filtered barcodes for sample 01
    # filteredBcIndex <- tstrsplit(colData(tenx)[, "Barcode"], "-")[[2]] == 1
    # filteredBc <- colData(tenx)[filteredBcIndex, ][["Barcode"]]

    filteredBc <- system.file("extdata",
        "SRR5167880_E18_20160930_Neurons_Sample_01_filtered_barcode.tsv",
        package = "scruff")
    # QC results are saved to current working directory
    sce <- tenxBamqc(bam = bamfile10x,
        experiment = "Neurons_Sample_01",
        filter = filteredBc)
    sce

[Package scruff version 1.5.12 Index]