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Commands log parsing functions

Source: R/commands.R
commands.Rd

Commands log parsing functions

Usage

getBarcodeCutoffFromCommands(log)

getLevelFromCommands(log)

getUmiTypeFromCommands(log)

Arguments

log

character. Commands log.

Value

atomic.

Functions

  • getBarcodeCutoffFromCommands(): integer(1).

  • getLevelFromCommands(): character(1). Return "genes" or "transcripts".

  • getUmiTypeFromCommands(): character(1).

Note

Updated 2023-09-21.

Author

Michael Steinbaugh, Rory Kirchner

Examples

file <- file.path(bcbioBaseTestsUrl, "surecell-commands.log")
log <- import(file)
#> → Downloading <https://r.acidgenomics.com/testdata/bcbiobase/surecell-commands.log> to /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmprBcLWH/c25lHsA3v1-169651164251099/pipette-10f0e549d60e0.log.
#> → Importing <https://r.acidgenomics.com/testdata/bcbiobase/surecell-commands.log> using base::`readLines()`.
getBarcodeCutoffFromCommands(log)
#> ℹ 1000 reads per cellular barcode cutoff detected.
#> [1] 1000
getLevelFromCommands(log)
#> Counts will imported as genes.
#> [1] "genes"
getUmiTypeFromCommands(log)
#> UMI type: surecell
#> [1] "surecell"