fragpipe_find_psm_files: Helper function to find psm.tsv files within a FragPipe...
In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline
View source: R/parse_fragpipe.R
fragpipe_find_psm_files R Documentation
Helper function to find psm.tsv files within a FragPipe output directory
Description
File "filelist_ionquant.txt" contains a list of all psm.tsv files that are part of this dataset.
In older FragPipe versions, e.g. 15.0, this file is not available.
If filelist_ionquant.txt is available, extract listed psm.tsv files. If ALL of these are valid paths
for files within the provided FragPipe output directory (path parameter); assume this is the list
of PSM files we need. Print a warning if the table is in invalid format or if any of the listed
PSM files cannot be found within path.
As a fallback, search all direct subdirectories (i.e. not recursive) of path for psm.tsv files.
Usage
fragpipe_find_psm_files(path)
Arguments
path
FragPipe output directory
ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.
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View source: R/parse_fragpipe.R
| fragpipe_find_psm_files | R Documentation |
Helper function to find psm.tsv files within a FragPipe output directory
Description
File "filelist_ionquant.txt" contains a list of all psm.tsv files that are part of this dataset. In older FragPipe versions, e.g. 15.0, this file is not available.
If filelist_ionquant.txt is available, extract listed psm.tsv files. If ALL of these are valid paths
for files within the provided FragPipe output directory (path parameter); assume this is the list
of PSM files we need. Print a warning if the table is in invalid format or if any of the listed
PSM files cannot be found within path.
As a fallback, search all direct subdirectories (i.e. not recursive) of path for psm.tsv files.
Usage
fragpipe_find_psm_files(path)
Arguments
path |
FragPipe output directory |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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