Skip to content

tests(converters): fix spectronaut and metamorpheus tests #117

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
tonywu1999 merged 2 commits into from
Aug 4, 2025
Merged

tests(converters): fix spectronaut and metamorpheus tests #117

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
154a72b
tests(converters): fix spectronaut and metamorpheus tests
tonywu1999 Aug 4, 2025
2935a93
fix docs with terminus
tonywu1999 Aug 4, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions R/MSstatsPTM.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,6 @@
#' analysis and summarization
#' }
#'
#' @docType package
#' @name MSstatsPTM
NULL
#' @keywords internal
"_PACKAGE"
60 changes: 32 additions & 28 deletions R/converters.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1450,22 +1450,26 @@ SpectronauttoMSstatsPTMFormat = function(
bracket="[",
replace_text=TRUE)

ptm_input = SpectronauttoMSstatsFormat(input, annotation, intensity,
filter_with_Qvalue,
qvalue_cutoff, useUniquePeptide,
removeFewMeasurements,
removeProtein_with1Feature,
summaryforMultipleRows)
ptm_input = SpectronauttoMSstatsFormat(input, annotation,
intensity = intensity,
filter_with_Qvalue = filter_with_Qvalue,
qvalue_cutoff = qvalue_cutoff,
useUniquePeptide = useUniquePeptide,
removeFewMeasurements = removeFewMeasurements,
removeProtein_with1Feature = removeProtein_with1Feature,
summaryforMultipleRows = summaryforMultipleRows)

msstats_input = list(PTM = ptm_input)
if (!is.null(protein_input)) {
protein_input = SpectronauttoMSstatsFormat(protein_input,
annotation_protein, intensity,
filter_with_Qvalue,
qvalue_cutoff, useUniquePeptide,
removeFewMeasurements,
removeProtein_with1Feature,
summaryforMultipleRows)
annotation_protein,
intensity = intensity,
filter_with_Qvalue = filter_with_Qvalue,
qvalue_cutoff = qvalue_cutoff,
useUniquePeptide = useUniquePeptide,
removeFewMeasurements = removeFewMeasurements,
removeProtein_with1Feature = removeProtein_with1Feature,
summaryforMultipleRows = summaryforMultipleRows)

msstats_input = list(PTM = ptm_input, PROTEIN = protein_input)
}
Expand Down Expand Up @@ -1598,28 +1602,28 @@ MetamorpheusToMSstatsPTMFormat = function(input,

ptm_input = MetamorpheusToMSstatsFormat(input,
annotation,
useUniquePeptide,
removeFewMeasurements,
removeProtein_with1Feature,
summaryforMultipleRows,
use_log_file,
append,
verbose,
log_file_path)
useUniquePeptide = useUniquePeptide,
removeFewMeasurements = removeFewMeasurements,
removeProtein_with1Feature = removeProtein_with1Feature,
summaryforMultipleRows = summaryforMultipleRows,
use_log_file = use_log_file,
append = append,
verbose = verbose,
log_file_path = log_file_path)

msstats_format = list(PTM = ptm_input, PROTEIN = NULL)

if (!is.null(input_protein)) {
protein_input = MetamorpheusToMSstatsFormat(input_protein,
annotation_protein,
useUniquePeptide,
removeFewMeasurements,
removeProtein_with1Feature,
summaryforMultipleRows,
use_log_file,
append,
verbose,
log_file_path)
useUniquePeptide = useUniquePeptide,
removeFewMeasurements = removeFewMeasurements,
removeProtein_with1Feature = removeProtein_with1Feature,
summaryforMultipleRows = summaryforMultipleRows,
use_log_file = use_log_file,
append = append,
verbose = verbose,
log_file_path = log_file_path)

ptm_input = ptm_input[grepl(mod_id, ptm_input$PeptideSequence),]

Expand Down
13 changes: 8 additions & 5 deletions R/utils_converters.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -609,11 +609,14 @@ MSstatsPTMSiteLocator = function(data,

return(data)
}
#' Add site location and aa
#' @param data data.table
#' @param fasta_file string or data.table
#' @return data.table
#' @keywords internal

#' Fix terminus location adjustments
#' @param data data.table containing peptide data
#' @param terminus_id character string identifying the terminus
#' (e.g. N-terminus)
#' @param unmod_pep_col character string specifying the column name containing
#' unmodified peptide sequences
#' @return data.table with corrected Start positions
.fixTerminus = function(data, terminus_id, unmod_pep_col){

## Terminus makes start location off
Expand Down
Loading
Loading