params |
Named list of parameters with components:
-
study : String used to name the output directory within parentDir .
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metadata : Named list with components:
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run : Logical indicating whether to fetch metadata. See
fetchMetadata() . If TRUE , saves a file
parentDir /study /metadata.csv. If FALSE , expects that file to
already exist. The unmodified fetched or found metadata is saved to a
file parentDir /study /metadata_original.csv. 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 files from SRA. See fetch() .
If TRUE , saves files to parentDir /study /fetch_output. Whether
TRUE or FALSE , expects metadata to have a column "run_accession", and
updates metadata with column "fastq_fetched" containing paths to files in
parentDir /study /fetch_output. Following components are only checked
if run is TRUE .
-
keep : Logical indicating whether to keep fastq.gz files when all
processing steps have completed. NULL indicates TRUE .
-
overwrite : Logical indicating whether to overwrite files that already
exist. NULL indicates to use the default in fetch() .
-
keepSra : Logical indicating whether to keep the ".sra" files. NULL
indicates to use the default in fetch() .
-
prefetchCmd : String indicating command for prefetch, which downloads
".sra" files. NULL indicates to use the default in fetch() .
-
prefetchArgs : Character vector indicating arguments to pass to
prefetch. NULL indicates to use the default in fetch() .
-
fasterqdumpCmd : String indicating command for fasterq-dump, which
uses ".sra" files to create ".fastq" files. NULL indicates to use the
default in fetch() .
-
prefetchArgs : Character vector indicating arguments to pass to
fasterq-dump. NULL indicates to use the default in fetch() .
-
pigzCmd : String indicating command for pigz, which converts ".fastq"
files to ".fastq.gz" files. NULL indicates to use the default in
fetch() .
-
pigzArgs : Character vector indicating arguments to pass to pigz. 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 .
-
keep : Logical indicating whether to keep trimmed fastq files when all
processing steps have completed. NULL indicates 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() .
-
pigzCmd : String indicating command for pigz, which converts ".fastq"
files to ".fastq.gz" files. 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 .
-
keep : Logical indicating whether to keep fastqc files when all
processing steps have completed. NULL indicates 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 ,
saves results to parentDir /study /salmon_output and
parentDir /study /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.
-
sampleColname : String indicating column in metadata containing sample
ids. NULL indicates "sample_accession", which should work for data
from SRA and ENA.
-
keep : Logical indicating whether to keep quantification results when
all processing steps have completed. NULL indicates TRUE .
-
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
metadata to have a column sampleColname of sample ids, and expects a
directory parentDir /study /salmon_output containing directories of
quantification results, and saves results to
parentDir /study /tximport_output.qs. If FALSE , expects and does
nothing. Following components are only checked if run is TRUE .
-
tx2gene : Optional named list with components:
-
organism : String indicating organism and thereby ensembl gene dataset.
See getTx2gene() .
-
version : Optional number indicating ensembl version. NULL indicates
the latest version. See getTx2gene() .
-
filename : Optional string indicating name of pre-existing text file
in parentDir /params$study containing mapping between transcripts
(first column) and genes (second column), with column names in the
first row. If filename is specified, organism and version must not
be specified.
If not NULL , saves a file parentDir /study /tx2gene.csv.gz.
-
countsFromAbundance : String indicating whether or how to estimate
counts using estimated abundances. See tximport::tximport() .
-
ignoreTxVersion : Logical indicating whether to the version suffix on
transcript ids. NULL indicates to use TRUE . See
tximport::tximport() .
params can be derived from a yaml file, see
vignette("introduction", package = "seeker") . The yaml representation
of params will be saved to parentDir /params$study /params.yml.
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