| params |
Named list of parameters with components:
study: String used to name the output directory within parentDir.
metadata: Named list with components:
run: Logical indicating whether to fetch metadata from ENA. See
fetchMetadata(). If TRUE, saves a file
parentDir/study/data/metadata.csv. If FALSE, expects that file to
already exist. Following components are only checked if run is TRUE.
bioproject: String indicating the study's bioproject accession.
include: Optional named list for specifying which rows of metadata to
include for further processing, with components:
exclude: Optional named list for specifying which rows of metadata to
exclude from further processing (superseding include), with components:
fetch: Named list with components:
run: Logical indicating whether to fetch fastq(.gz) files using ascp.
See fetch(). If TRUE, expects metadata to have a column
'fastq_aspera' containing remote paths, and saves files to
parentDir/study/fetch_output. If FALSE, expects metadata to have a
column 'fastq_aspera' containing names (or complete paths, local or
remote) of fastq files. Whether TRUE or FALSE, updates metadata with
column 'fastq_fetched' containing paths to files that should be in
parentDir/study/fetch_output. Following components are only checked
if run is TRUE.
overwrite: Logical indicating whether to overwrite files that already
exist. NULL indicates to use the default in fetch().
ascpCmd: String indicating path to ascp. NULL indicates to use the
default in fetch().
ascpArgs: Character vector of arguments to pass to ascp. NULL
indicates to use the default in fetch().
ascpPrefix: String indicating prefix for fetching files. NULL
indicates to use the default in fetch().
trimgalore: Named list with components:
run: Logical indicating whether to perform quality/adapter trimming of
reads. See trimgalore(). If TRUE, expects metadata to have a column
'fastq_fetched' containing paths to fastq files in
parentDir/study/fetch_output, saves trimmed files to
parentDir/study/trimgalore_output, and updates metadata with column
'fastq_trimmed'. If FALSE, expects and does nothing. Following
components are only checked if run is TRUE.
cmd: Name or path of the command-line interface. NULL indicates to
use the default in trimgalore().
args: Additional arguments to pass to the command-line interface.
NULL indicates to use the default in trimgalore().
fastqc: Named list with components:
run: Logical indicating whether to perform QC on reads. See fastqc().
If TRUE and trimgalore$run is TRUE, expects metadata to have a
column 'fastq_trimmed' containing paths to fastq files in
parentDir/study/trimgalore_output. If TRUE and trimgalore$run is
FALSE, expects metadata to have a column 'fastq_fetched' containing
paths to fastq files in parentDir/study/fetch_output. If TRUE,
saves results to parentDir/study/fastqc_output. If FALSE, expects
and does nothing. Following components are only checked if run is
TRUE.
cmd: Name or path of the command-line interface. NULL indicates to
use the default in fastqc().
args: Additional arguments to pass to the command-line interface.
NULL indicates to use the default in fastqc().
salmon: Named list with components:
run: Logical indicating whether to quantify transcript abundances. See
salmon(). If TRUE and trimgalore$run is TRUE, expects metadata to
have a column 'fastq_trimmed' containing paths to fastq files in
parentDir/study/trimgalore_output. If TRUE and trimgalore$run is
FALSE, expects metadata to have a column 'fastq_fetched' containing
paths to fastq files in parentDir/study/fetch_output. If TRUE, also
expects metadata to have a column 'sample_accession' containing sample
ids, and saves results to parentDir/study/salmon_output and
parentDir/study/data/salmon_meta_info.csv. If FALSE, expects and
does nothing. Following components are only checked if run is TRUE.
indexDir: Directory that contains salmon index.
cmd: Name or path of the command-line interface. NULL indicates to
use the default in salmon().
args: Additional arguments to pass to the command-line interface.
NULL indicates to use the default in salmon().
multiqc: Named list with components:
run: Logical indicating whether to aggregrate results of various
processing steps. See multiqc(). If TRUE, saves results to
parentDir/study/multiqc_output. If FALSE, expects and does nothing.
Following components are only checked if run is TRUE.
cmd: Name or path of the command-line interface. NULL indicates to
use the default in multiqc().
args: Additional arguments to pass to the command-line interface.
NULL indicates to use the default in multiqc().
tximport: Named list with components:
run: Logical indicating whether to summarize transcript- or gene-level
estimates for downstream analysis. See tximport(). If TRUE, expects a
directory parentDir/study/salmon_output containing directories of
quantification results from salmon, and saves results to
parentDir/study/data/tximport_output.qs. If FALSE, expects and does
nothing. Following components are only checked if run is TRUE.
tx2gene: Optional named list with components:
If specified, saves a file parentDir/study/data/tx2gene.csv. countsFromAbundance: String indicating whether or how to estimate
counts using estimated abundances. See tximport::tximport().
ignoreTxVersion: Logical indicating whether to the version suffix on
transcript ids. If NULL, indicates to use TRUE. See
tximport::tximport().
params can be derived from a yaml file, see
vignette('introduction', package = 'seeker'). The yaml representation
of params will be saved to parentDir/params$study/data/params.yml.
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