prepareSalmonFilesDataFrame: Prepare data.frame needed run importSalmonData.

In kvittingseerup/IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Prepare data.frame needed run importSalmonData.

Description

An easy to use wrapper for creating the "salmonFileDataFrame" data.frame needed to run importSalmonData.

Usage

prepareSalmonFileDataFrame(
    ### Core arguments
    parentDir,

    ### Advanced arguments
    pattern='',
    invertPattern=FALSE,
    ignore.case=FALSE,
    quiet = FALSE
)

Arguments

parentDir	Parent directory where each quantified sample is in a sub-directory. The function will then look for files containing the (suffix) of the default files names for the quantification tools. The suffixes identified are 'abundance.tsv' for Kallisto, 'quant.sf' for Salmon, 'isoforms.results' for RSEM and 't_data.ctab' for StringTie. This is an alternative to sampleVector (aka only one of them should be used).
pattern	A character string containing a regular expression for which files to import (applied to full path). Default is "" corresponding to all. See base::grepl for more details.
invertPattern	A Logical. If TRUE only use files which do not match the pattern argument.
ignore.case	A logical. If TRUE case is ignored duing matching with the pattern argument. If FALSE the matching with the pattern argument is case sensitive.
quiet	A logic indicating whether to avoid printing progress messages (incl. progress bar). Default is FALSE

Value

The data.frame with 3 columns.

• Column 1: "files". Contains the file each found in subdirectiories of the parentDir directory.

• Column 2: "names". The name of the subdirectory.

• Column 3: "condition". Set to NA as the function does not attemp to guess conditions. To use importSalmonData you will need to add these manually.

Author(s)

Kristoffer Vitting-Seerup

References

Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

See Also

importSalmonData

Examples

### Please note
# The way of importing files in the following example with
#   "system.file('pathToFile', package="IsoformSwitchAnalyzeR") is
#   specialized way of accessing the example data in the IsoformSwitchAnalyzeR package
#   and not something you need to do - just supply the string e.g.
#   parentDir = "individual_quantifications_in_subdir/" to the functions
#   path (e.g. "myAnnotation/isoformsQuantified.gtf") to the isoformExonAnnoation argument

### Prepare data.frame with quant file info
salmonDf <- prepareSalmonFileDataFrame(
    system.file("extdata/drosophila", package="IsoformSwitchAnalyzeR")
)

### Add conditions
salmonDf$condition <- c('wt','wt','ko','ko')

### Create switchAnalyzeRlist
aSwitchList <- importSalmonData(salmonDf)

kvittingseerup/IsoformSwitchAnalyzeR documentation built on Jan. 14, 2024, 11:30 p.m.