inst/tinytest/test_converters.R
In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications
## Utility functions
#' Validate positive number of rows from converter output
#'
#' @author Anthony Wu
#'
#' @param msstats_ptm_input A list containing PTM and PROTEIN data tables
.validatePositiveNumberOfRows = function(msstats_ptm_input) {
expect_true(nrow(msstats_ptm_input$PTM) > 0)
expect_true(nrow(msstats_ptm_input$PROTEIN) > 0)
}
#' Validate protein ID count in converter output
#'
#' @author Anthony Wu
#'
#' @param msstats_input Either PTM or PROTEIN data tables
#' @param protein_id Protein ID to validate
#' @param count Expected count of protein ID in ProteinName column
.validateProteinId = function(msstats_input, protein_id, count) {
expect_equal(length(which(msstats_input$ProteinName==protein_id)), count)
}
#' Validate ptm ID count in converter output
#'
#' @author Anthony Wu
#'
#' @param msstats_input Either PTM or PROTEIN data tables
#' @param ptm_substring PTM to validate
#' @param count Expected count of PTM in PeptideSequence column
.validatePtmSubstring = function(msstats_input, ptm_substring, count) {
expect_equal(
length(which(grepl(ptm_substring, msstats_input$PeptideSequence))),
count
)
}
## MaxQ TMT
data("maxq_tmt_evidence", package = "MSstatsPTM")
data("maxq_tmt_annotation", package = "MSstatsPTM")
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
use_unmod_peptides=TRUE,
labeling_type = "TMT"))
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
use_unmod_peptides=FALSE,
labeling_type = "TMT"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta_protein_name="uniprot_ac",
use_unmod_peptides=FALSE,
labeling_type = "TMT"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
fasta_protein_name="uniprot_ac",
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=FALSE,
labeling_type = "TMT"))
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
use_unmod_peptides=FALSE,
labeling_type = "TMT",
removeOxidationMpeptides=TRUE))
mq_imported = MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
use_unmod_peptides=TRUE,
labeling_type = "TMT")
.validatePositiveNumberOfRows(mq_imported)
.validateProteinId(mq_imported$PROTEIN, "P29966", 10)
.validateProteinId(mq_imported$PTM, "P29966_T150", 70)
.validateProteinId(mq_imported$PTM, "P29966_T143_S145", 10)
.validatePtmSubstring(
mq_imported$PTM, "Phospho \\(STY\\)",
length(mq_imported$PTM$PeptideSequence))
.validatePtmSubstring(
mq_imported$PROTEIN, "Phospho \\(STY\\)", 0)
## MaxQ LF
data("maxq_lf_evidence", package = "MSstatsPTM")
data("maxq_lf_annotation", package = "MSstatsPTM")
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "LF",
which_proteinid_ptm = "Proteins"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "TMT",
which_proteinid_ptm = "Proteins"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "TMT",
which_proteinid_ptm = "Proteins"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "TMT",
which_proteinid_ptm = "Leading.proteins"))
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=FALSE,
labeling_type = "LF",
which_proteinid_ptm = "Proteins"))
mq_imported = MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "LF",
which_proteinid_ptm = "Proteins")
.validatePositiveNumberOfRows(mq_imported)
.validateProteinId(mq_imported$PROTEIN, "P36578", 144)
.validateProteinId(mq_imported$PTM, "P36578_S295", 72)
.validateProteinId(mq_imported$PTM, "Q13523_S431_S437", 36)
.validatePtmSubstring(
mq_imported$PTM, "Phospho \\(STY\\)",
length(mq_imported$PTM$PeptideSequence))
.validatePtmSubstring(
mq_imported$PROTEIN, "Phospho \\(STY\\)", 0)
## Spectronaut
data("spectronaut_input", package = "MSstatsPTM")
data("spectronaut_annotation", package = "MSstatsPTM")
expect_silent(SpectronauttoMSstatsPTMFormat(spectronaut_input,
annotation=spectronaut_annotation,
fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=TRUE,
mod_id = "\\[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
))
expect_error(SpectronauttoMSstatsPTMFormat(spectronaut_input,
annotation=spectronaut_annotation,
use_unmod_peptides=TRUE,
mod_id = "[[[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
))
expect_silent(SpectronauttoMSstatsPTMFormat(spectronaut_input,
fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=TRUE,
mod_id = "\\[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
))
expect_silent(SpectronauttoMSstatsPTMFormat(spectronaut_input,
annotation=spectronaut_annotation,
fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"),
mod_id = "\\[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
))
spectronaut_imported = SpectronauttoMSstatsPTMFormat(spectronaut_input,
annotation=spectronaut_annotation,
fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=TRUE,
mod_id = "\\[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
)
.validatePositiveNumberOfRows(spectronaut_imported)
.validateProteinId(spectronaut_imported$PROTEIN, "P36578", 36)
.validateProteinId(spectronaut_imported$PTM, "P36578_S295", 36)
.validateProteinId(spectronaut_imported$PTM, "P09938_S15_S22", 36)
.validatePtmSubstring(
spectronaut_imported$PTM, "Phospho \\(STY\\)",
length(spectronaut_imported$PTM$PeptideSequence))
.validatePtmSubstring(
spectronaut_imported$PROTEIN, "Phospho \\(STY\\)", 0)
## PD
data("pd_psm_input", package = "MSstatsPTM")
data("pd_annotation", package = "MSstatsPTM")
data("pd_testing_output", package = "MSstatsPTM")
expect_message(PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions"))
expect_equal(pd_testing_output, PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions"))
expect_equal(pd_testing_output, PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions"))
expect_message(PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions",
use_localization_cutoff = FALSE))
expect_error(PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions"))
expect_message(PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
which_proteinid = "Master.Protein.Accessions"))
expect_error(PDtoMSstatsPTMFormat(pd_psm_input,
NULL,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
which_proteinid = "Master.Protein.Accessions"))
expect_error(PDtoMSstatsPTMFormat(pd_psm_input,
data.frame(columns=c("Condition", "BioReplicate")),
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
which_proteinid = "Master.Protein.Accessions"))
input = system.file("tinytest/raw_data/PD/pd-ptm-input.csv",
package = "MSstatsPTM")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/PD/pd-ptm-annot.csv",
package = "MSstatsPTM")
annot = data.table::fread(annot)
input_protein = system.file("tinytest/raw_data/PD/protein-input.csv",
package = "MSstatsPTM")
input_protein = data.table::fread(input_protein)
annot_protein = system.file("tinytest/raw_data/PD/protein-annot.csv",
package = "MSstatsPTM")
annot_protein = data.table::fread(annot_protein)
fasta_path=system.file("extdata", "pd_with_proteome.fasta",
package="MSstatsPTM")
pd_imported = PDtoMSstatsPTMFormat(
input,
annotation = annot,
protein_input = input_protein,
annotation_protein = annot_protein,
fasta_path = fasta_path,
mod_id = "\\(GG\\)",
labeling_type = "TMT",
use_localization_cutoff = FALSE,
which_proteinid = "Master.Protein.Accessions")
.validatePositiveNumberOfRows(pd_imported)
.validateProteinId(pd_imported$PROTEIN, "P52480", 30)
.validateProteinId(pd_imported$PTM, "P52480_K305", 12)
.validateProteinId(pd_imported$PTM, "P52480", 0)
.validatePtmSubstring(
pd_imported$PTM, "\\*",
length(pd_imported$PTM$PeptideSequence))
.validatePtmSubstring(
pd_imported$PROTEIN, "\\*", 0)
## Metamorpheus
#### Setup
input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv",
package = "MSstatsPTM")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv",
package = "MSstatsPTM")
annot = data.table::fread(annot)
input_protein = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaksGlobalProteome.tsv",
package = "MSstatsPTM")
input_protein = data.table::fread(input_protein)
annot_protein = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesignGlobalProteome.tsv",
package = "MSstatsPTM")
annot_protein = data.table::fread(annot_protein)
fasta_path=system.file("extdata", "metamorpheus_fasta.fasta",
package="MSstatsPTM")
#### Happy Case
expect_silent(MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
input_protein=input_protein,
annotation_protein=annot_protein,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### Global profiling run removed
expect_silent(MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
use_unmod_peptides = FALSE,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### Global profiling run removed with use_unmod_peptides = TRUE
expect_silent(MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
use_unmod_peptides = TRUE,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### FASTA file missing
expect_error(MetamorpheusToMSstatsPTMFormat(
input,
annot,
input_protein=input_protein,
annotation_protein=annot_protein,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### Annotation missing
expect_error(MetamorpheusToMSstatsPTMFormat(
input,
fasta_path=fasta_path,
input_protein=input_protein,
annotation_protein=annot_protein,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### Output validation tests
metamorpheus_imported = MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
input_protein=input_protein,
annotation_protein=annot_protein,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
)
.validatePositiveNumberOfRows(metamorpheus_imported)
.validateProteinId(metamorpheus_imported$PROTEIN, "O95817", 12)
.validateProteinId(metamorpheus_imported$PTM, "O95817_C207", 6)
.validateProteinId(metamorpheus_imported$PTM, "O95817", 0)
.validatePtmSubstring(
metamorpheus_imported$PTM, "\\[Common Fixed:Carbamidomethyl on C\\]",
length(metamorpheus_imported$PTM$PeptideSequence))
.validatePtmSubstring(
metamorpheus_imported$PROTEIN, "\\[Common Fixed:Carbamidomethyl on C\\]", 0)
metamorpheus_imported = MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
use_unmod_peptides = TRUE,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
)
.validatePositiveNumberOfRows(metamorpheus_imported)
.validateProteinId(metamorpheus_imported$PROTEIN, "O95817", 6)
.validateProteinId(metamorpheus_imported$PTM, "O95817_C207", 6)
.validateProteinId(metamorpheus_imported$PTM, "O95817", 0)
.validatePtmSubstring(
metamorpheus_imported$PTM, "\\[Common Fixed:Carbamidomethyl on C\\]",
length(metamorpheus_imported$PTM$PeptideSequence))
.validatePtmSubstring(
metamorpheus_imported$PROTEIN, "\\[Common Fixed:Carbamidomethyl on C\\]", 0)
# Progenesis
input = system.file("tinytest/raw_data/Progenesis/progenesis_peptide.csv",
package = "MSstatsPTM")
input = data.table::fread(input)
colnames(input) = unlist(input[1,])
input = input[-1,]
annot = system.file("tinytest/raw_data/Progenesis/phospho_annotation.csv",
package = "MSstatsPTM")
annot = data.table::fread(annot)
expect_silent(ProgenesistoMSstatsPTMFormat(
input,
annot,
))
expect_error(ProgenesistoMSstatsPTMFormat(
input
))
prog_imported = ProgenesistoMSstatsPTMFormat(
input,
annot,
)
.validateProteinId(prog_imported$PTM,
"sp|A2ASS6|TITIN_MOUSE_AVTSPPRVKSPEPR_[4] Phospho (ST)|[10] Phospho (ST)",
18
)
# Fragpipe
#### Happy Case
expect_silent(FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_annotation,
fragpipe_input_protein,
fragpipe_annotation_protein,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE)
)
#### Global profiling run removed
expect_silent(FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_annotation,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE)
)
#### use_unmod_peptides = TRUE, no unmodified proteins in dataset
expect_error(FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_annotation,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE,
use_unmod_peptides=TRUE)
)
#### Annotation missing
expect_error(FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_input_protein,
fragpipe_annotation_protein,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE)
)
fragpipe_input = FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_annotation,
fragpipe_input_protein,
fragpipe_annotation_protein,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE)
.validatePositiveNumberOfRows(fragpipe_input)
.validateProteinId(fragpipe_input$PROTEIN, "sp|Q9Y2W1|TR150_HUMAN", 110)
.validateProteinId(fragpipe_input$PTM, "sp|Q9Y2W1|TR150_HUMAN_S805", 20)
.validateProteinId(fragpipe_input$PTM, "sp|Q9Y2W1|TR150_HUMAN_S248_S253", 20)
.validatePtmSubstring(
fragpipe_input$PTM, "\\*",
length(fragpipe_input$PTM$PeptideSequence))
.validatePtmSubstring(
fragpipe_input$PROTEIN, "\\*", 0)
# LFQ Example (w/out global profiling run)
input = system.file("tinytest/raw_data/Fragpipe/MSstats.csv",
package = "MSstatsPTM")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/Fragpipe/experiment_annotation.tsv",
package = "MSstatsPTM")
annot = data.table::fread(annot)
#### Happy Case
expect_silent(FragPipetoMSstatsPTMFormat(input,
annot,
label_type="LF",
mod_id_col = "STY",
localization_cutoff=.75,
protein_id_col = "ProteinName",
peptide_id_col = "PeptideSequence")
)
#### Annotation file not provided but present in input
expect_silent(FragPipetoMSstatsPTMFormat(input,
label_type="LF",
mod_id_col = "STY",
localization_cutoff=.75,
protein_id_col = "ProteinName",
peptide_id_col = "PeptideSequence")
)
fragpipe_input = FragPipetoMSstatsPTMFormat(input,
annot,
label_type="LF",
mod_id_col = "STY",
localization_cutoff=.75,
protein_id_col = "ProteinName",
peptide_id_col = "PeptideSequence")
.validateProteinId(fragpipe_input$PTM, "sp|P02400|RLA4_YEAST_S100", 8)
.validateProteinId(fragpipe_input$PTM, "sp|O13563|RPN13_YEAST_S132", 4)
.validatePtmSubstring(
fragpipe_input$PTM, "\\*",
length(fragpipe_input$PTM$PeptideSequence))
Vitek-Lab/MSstatsPTM documentation built on Sept. 26, 2024, 9:28 p.m.
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## Utility functions
#' Validate positive number of rows from converter output
#'
#' @author Anthony Wu
#'
#' @param msstats_ptm_input A list containing PTM and PROTEIN data tables
.validatePositiveNumberOfRows = function(msstats_ptm_input) {
expect_true(nrow(msstats_ptm_input$PTM) > 0)
expect_true(nrow(msstats_ptm_input$PROTEIN) > 0)
}
#' Validate protein ID count in converter output
#'
#' @author Anthony Wu
#'
#' @param msstats_input Either PTM or PROTEIN data tables
#' @param protein_id Protein ID to validate
#' @param count Expected count of protein ID in ProteinName column
.validateProteinId = function(msstats_input, protein_id, count) {
expect_equal(length(which(msstats_input$ProteinName==protein_id)), count)
}
#' Validate ptm ID count in converter output
#'
#' @author Anthony Wu
#'
#' @param msstats_input Either PTM or PROTEIN data tables
#' @param ptm_substring PTM to validate
#' @param count Expected count of PTM in PeptideSequence column
.validatePtmSubstring = function(msstats_input, ptm_substring, count) {
expect_equal(
length(which(grepl(ptm_substring, msstats_input$PeptideSequence))),
count
)
}
## MaxQ TMT
data("maxq_tmt_evidence", package = "MSstatsPTM")
data("maxq_tmt_annotation", package = "MSstatsPTM")
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
use_unmod_peptides=TRUE,
labeling_type = "TMT"))
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
use_unmod_peptides=FALSE,
labeling_type = "TMT"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta_protein_name="uniprot_ac",
use_unmod_peptides=FALSE,
labeling_type = "TMT"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
fasta_protein_name="uniprot_ac",
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=FALSE,
labeling_type = "TMT"))
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
use_unmod_peptides=FALSE,
labeling_type = "TMT",
removeOxidationMpeptides=TRUE))
mq_imported = MaxQtoMSstatsPTMFormat(evidence=maxq_tmt_evidence,
annotation=maxq_tmt_annotation,
fasta=system.file("extdata", "maxq_tmt_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
use_unmod_peptides=TRUE,
labeling_type = "TMT")
.validatePositiveNumberOfRows(mq_imported)
.validateProteinId(mq_imported$PROTEIN, "P29966", 10)
.validateProteinId(mq_imported$PTM, "P29966_T150", 70)
.validateProteinId(mq_imported$PTM, "P29966_T143_S145", 10)
.validatePtmSubstring(
mq_imported$PTM, "Phospho \\(STY\\)",
length(mq_imported$PTM$PeptideSequence))
.validatePtmSubstring(
mq_imported$PROTEIN, "Phospho \\(STY\\)", 0)
## MaxQ LF
data("maxq_lf_evidence", package = "MSstatsPTM")
data("maxq_lf_annotation", package = "MSstatsPTM")
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "LF",
which_proteinid_ptm = "Proteins"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "TMT",
which_proteinid_ptm = "Proteins"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "TMT",
which_proteinid_ptm = "Proteins"))
expect_error(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "TMT",
which_proteinid_ptm = "Leading.proteins"))
expect_silent(MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=FALSE,
labeling_type = "LF",
which_proteinid_ptm = "Proteins"))
mq_imported = MaxQtoMSstatsPTMFormat(evidence=maxq_lf_evidence,
annotation=maxq_lf_annotation,
fasta=system.file("extdata", "maxq_lf_fasta.fasta", package="MSstatsPTM"),
fasta_protein_name="uniprot_ac",
mod_id="\\(Phospho \\(STY\\)\\)",
use_unmod_peptides=TRUE,
labeling_type = "LF",
which_proteinid_ptm = "Proteins")
.validatePositiveNumberOfRows(mq_imported)
.validateProteinId(mq_imported$PROTEIN, "P36578", 144)
.validateProteinId(mq_imported$PTM, "P36578_S295", 72)
.validateProteinId(mq_imported$PTM, "Q13523_S431_S437", 36)
.validatePtmSubstring(
mq_imported$PTM, "Phospho \\(STY\\)",
length(mq_imported$PTM$PeptideSequence))
.validatePtmSubstring(
mq_imported$PROTEIN, "Phospho \\(STY\\)", 0)
## Spectronaut
data("spectronaut_input", package = "MSstatsPTM")
data("spectronaut_annotation", package = "MSstatsPTM")
expect_silent(SpectronauttoMSstatsPTMFormat(spectronaut_input,
annotation=spectronaut_annotation,
fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=TRUE,
mod_id = "\\[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
))
expect_error(SpectronauttoMSstatsPTMFormat(spectronaut_input,
annotation=spectronaut_annotation,
use_unmod_peptides=TRUE,
mod_id = "[[[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
))
expect_silent(SpectronauttoMSstatsPTMFormat(spectronaut_input,
fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=TRUE,
mod_id = "\\[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
))
expect_silent(SpectronauttoMSstatsPTMFormat(spectronaut_input,
annotation=spectronaut_annotation,
fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"),
mod_id = "\\[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
))
spectronaut_imported = SpectronauttoMSstatsPTMFormat(spectronaut_input,
annotation=spectronaut_annotation,
fasta_path=system.file("extdata", "spectronaut_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=TRUE,
mod_id = "\\[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso"
)
.validatePositiveNumberOfRows(spectronaut_imported)
.validateProteinId(spectronaut_imported$PROTEIN, "P36578", 36)
.validateProteinId(spectronaut_imported$PTM, "P36578_S295", 36)
.validateProteinId(spectronaut_imported$PTM, "P09938_S15_S22", 36)
.validatePtmSubstring(
spectronaut_imported$PTM, "Phospho \\(STY\\)",
length(spectronaut_imported$PTM$PeptideSequence))
.validatePtmSubstring(
spectronaut_imported$PROTEIN, "Phospho \\(STY\\)", 0)
## PD
data("pd_psm_input", package = "MSstatsPTM")
data("pd_annotation", package = "MSstatsPTM")
data("pd_testing_output", package = "MSstatsPTM")
expect_message(PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta", package="MSstatsPTM"),
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions"))
expect_equal(pd_testing_output, PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions"))
expect_equal(pd_testing_output, PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions"))
expect_message(PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions",
use_localization_cutoff = FALSE))
expect_error(PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
use_unmod_peptides=TRUE,
which_proteinid = "Master.Protein.Accessions"))
expect_message(PDtoMSstatsPTMFormat(pd_psm_input,
pd_annotation,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
which_proteinid = "Master.Protein.Accessions"))
expect_error(PDtoMSstatsPTMFormat(pd_psm_input,
NULL,
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
which_proteinid = "Master.Protein.Accessions"))
expect_error(PDtoMSstatsPTMFormat(pd_psm_input,
data.frame(columns=c("Condition", "BioReplicate")),
system.file("extdata", "pd_fasta.fasta",
package="MSstatsPTM"),
which_proteinid = "Master.Protein.Accessions"))
input = system.file("tinytest/raw_data/PD/pd-ptm-input.csv",
package = "MSstatsPTM")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/PD/pd-ptm-annot.csv",
package = "MSstatsPTM")
annot = data.table::fread(annot)
input_protein = system.file("tinytest/raw_data/PD/protein-input.csv",
package = "MSstatsPTM")
input_protein = data.table::fread(input_protein)
annot_protein = system.file("tinytest/raw_data/PD/protein-annot.csv",
package = "MSstatsPTM")
annot_protein = data.table::fread(annot_protein)
fasta_path=system.file("extdata", "pd_with_proteome.fasta",
package="MSstatsPTM")
pd_imported = PDtoMSstatsPTMFormat(
input,
annotation = annot,
protein_input = input_protein,
annotation_protein = annot_protein,
fasta_path = fasta_path,
mod_id = "\\(GG\\)",
labeling_type = "TMT",
use_localization_cutoff = FALSE,
which_proteinid = "Master.Protein.Accessions")
.validatePositiveNumberOfRows(pd_imported)
.validateProteinId(pd_imported$PROTEIN, "P52480", 30)
.validateProteinId(pd_imported$PTM, "P52480_K305", 12)
.validateProteinId(pd_imported$PTM, "P52480", 0)
.validatePtmSubstring(
pd_imported$PTM, "\\*",
length(pd_imported$PTM$PeptideSequence))
.validatePtmSubstring(
pd_imported$PROTEIN, "\\*", 0)
## Metamorpheus
#### Setup
input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv",
package = "MSstatsPTM")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv",
package = "MSstatsPTM")
annot = data.table::fread(annot)
input_protein = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaksGlobalProteome.tsv",
package = "MSstatsPTM")
input_protein = data.table::fread(input_protein)
annot_protein = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesignGlobalProteome.tsv",
package = "MSstatsPTM")
annot_protein = data.table::fread(annot_protein)
fasta_path=system.file("extdata", "metamorpheus_fasta.fasta",
package="MSstatsPTM")
#### Happy Case
expect_silent(MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
input_protein=input_protein,
annotation_protein=annot_protein,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### Global profiling run removed
expect_silent(MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
use_unmod_peptides = FALSE,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### Global profiling run removed with use_unmod_peptides = TRUE
expect_silent(MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
use_unmod_peptides = TRUE,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### FASTA file missing
expect_error(MetamorpheusToMSstatsPTMFormat(
input,
annot,
input_protein=input_protein,
annotation_protein=annot_protein,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### Annotation missing
expect_error(MetamorpheusToMSstatsPTMFormat(
input,
fasta_path=fasta_path,
input_protein=input_protein,
annotation_protein=annot_protein,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
))
#### Output validation tests
metamorpheus_imported = MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
input_protein=input_protein,
annotation_protein=annot_protein,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
)
.validatePositiveNumberOfRows(metamorpheus_imported)
.validateProteinId(metamorpheus_imported$PROTEIN, "O95817", 12)
.validateProteinId(metamorpheus_imported$PTM, "O95817_C207", 6)
.validateProteinId(metamorpheus_imported$PTM, "O95817", 0)
.validatePtmSubstring(
metamorpheus_imported$PTM, "\\[Common Fixed:Carbamidomethyl on C\\]",
length(metamorpheus_imported$PTM$PeptideSequence))
.validatePtmSubstring(
metamorpheus_imported$PROTEIN, "\\[Common Fixed:Carbamidomethyl on C\\]", 0)
metamorpheus_imported = MetamorpheusToMSstatsPTMFormat(
input,
annot,
fasta_path=fasta_path,
use_unmod_peptides = TRUE,
mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
)
.validatePositiveNumberOfRows(metamorpheus_imported)
.validateProteinId(metamorpheus_imported$PROTEIN, "O95817", 6)
.validateProteinId(metamorpheus_imported$PTM, "O95817_C207", 6)
.validateProteinId(metamorpheus_imported$PTM, "O95817", 0)
.validatePtmSubstring(
metamorpheus_imported$PTM, "\\[Common Fixed:Carbamidomethyl on C\\]",
length(metamorpheus_imported$PTM$PeptideSequence))
.validatePtmSubstring(
metamorpheus_imported$PROTEIN, "\\[Common Fixed:Carbamidomethyl on C\\]", 0)
# Progenesis
input = system.file("tinytest/raw_data/Progenesis/progenesis_peptide.csv",
package = "MSstatsPTM")
input = data.table::fread(input)
colnames(input) = unlist(input[1,])
input = input[-1,]
annot = system.file("tinytest/raw_data/Progenesis/phospho_annotation.csv",
package = "MSstatsPTM")
annot = data.table::fread(annot)
expect_silent(ProgenesistoMSstatsPTMFormat(
input,
annot,
))
expect_error(ProgenesistoMSstatsPTMFormat(
input
))
prog_imported = ProgenesistoMSstatsPTMFormat(
input,
annot,
)
.validateProteinId(prog_imported$PTM,
"sp|A2ASS6|TITIN_MOUSE_AVTSPPRVKSPEPR_[4] Phospho (ST)|[10] Phospho (ST)",
18
)
# Fragpipe
#### Happy Case
expect_silent(FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_annotation,
fragpipe_input_protein,
fragpipe_annotation_protein,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE)
)
#### Global profiling run removed
expect_silent(FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_annotation,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE)
)
#### use_unmod_peptides = TRUE, no unmodified proteins in dataset
expect_error(FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_annotation,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE,
use_unmod_peptides=TRUE)
)
#### Annotation missing
expect_error(FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_input_protein,
fragpipe_annotation_protein,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE)
)
fragpipe_input = FragPipetoMSstatsPTMFormat(fragpipe_input,
fragpipe_annotation,
fragpipe_input_protein,
fragpipe_annotation_protein,
label_type="TMT",
mod_id_col = "STY",
localization_cutoff=.75,
remove_unlocalized_peptides=TRUE)
.validatePositiveNumberOfRows(fragpipe_input)
.validateProteinId(fragpipe_input$PROTEIN, "sp|Q9Y2W1|TR150_HUMAN", 110)
.validateProteinId(fragpipe_input$PTM, "sp|Q9Y2W1|TR150_HUMAN_S805", 20)
.validateProteinId(fragpipe_input$PTM, "sp|Q9Y2W1|TR150_HUMAN_S248_S253", 20)
.validatePtmSubstring(
fragpipe_input$PTM, "\\*",
length(fragpipe_input$PTM$PeptideSequence))
.validatePtmSubstring(
fragpipe_input$PROTEIN, "\\*", 0)
# LFQ Example (w/out global profiling run)
input = system.file("tinytest/raw_data/Fragpipe/MSstats.csv",
package = "MSstatsPTM")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/Fragpipe/experiment_annotation.tsv",
package = "MSstatsPTM")
annot = data.table::fread(annot)
#### Happy Case
expect_silent(FragPipetoMSstatsPTMFormat(input,
annot,
label_type="LF",
mod_id_col = "STY",
localization_cutoff=.75,
protein_id_col = "ProteinName",
peptide_id_col = "PeptideSequence")
)
#### Annotation file not provided but present in input
expect_silent(FragPipetoMSstatsPTMFormat(input,
label_type="LF",
mod_id_col = "STY",
localization_cutoff=.75,
protein_id_col = "ProteinName",
peptide_id_col = "PeptideSequence")
)
fragpipe_input = FragPipetoMSstatsPTMFormat(input,
annot,
label_type="LF",
mod_id_col = "STY",
localization_cutoff=.75,
protein_id_col = "ProteinName",
peptide_id_col = "PeptideSequence")
.validateProteinId(fragpipe_input$PTM, "sp|P02400|RLA4_YEAST_S100", 8)
.validateProteinId(fragpipe_input$PTM, "sp|O13563|RPN13_YEAST_S132", 4)
.validatePtmSubstring(
fragpipe_input$PTM, "\\*",
length(fragpipe_input$PTM$PeptideSequence))
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