Description Usage Arguments Value Examples
Read BAM file generated by Cell Ranger pipeline and output QC metrics including number of aligned reads and reads aligned to an gene.
1 2 3 |
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 |
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>/. |
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
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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
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outDir |
Output directory. The location to write resulting QC table. |
cores |
Number of cores used for parallelization. Default is
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ggplot object showing the number of aligned reads and reads aligned to an gene.
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 | # 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
qcDt <- tenxBamqc(bam = bamfile10x,
experiment = "Neurons_Sample_01",
filter = filteredBc)
qcDt
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