SpectronauttoMSstatsPTMFormat | R Documentation |
Converters label-free Spectronaut data into MSstatsPTM format. Requires PSM output from Spectronaut and a custom made annotation file, mapping the run name to the condition and bioreplicate. Can optionally take a seperate PSM file for a global profiling run. If no global profiling run provided, the function can extract the unmodified peptides from the PTM PSM file and use them as a global profiling run (not recommended).
SpectronauttoMSstatsPTMFormat(
input,
annotation = NULL,
fasta_path = NULL,
protein_input = NULL,
annotation_protein = NULL,
use_unmod_peptides = FALSE,
intensity = "PeakArea",
mod_id = "\\[Phospho \\(STY\\)\\]",
fasta_protein_name = "uniprot_iso",
remove_other_mods = TRUE,
filter_with_Qvalue = TRUE,
qvalue_cutoff = 0.01,
useUniquePeptide = TRUE,
removeFewMeasurements = TRUE,
removeProtein_with1Feature = FALSE,
summaryforMultipleRows = max,
use_log_file = TRUE,
append = FALSE,
verbose = TRUE,
log_file_path = NULL
)
input |
name of Spectronaut PTM output, which is long-format. ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity, F.ExcludedFromQuantification are required. Rows with F.ExcludedFromQuantification=True will be removed. |
annotation |
name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Spectronaut, use annotation=NULL (default). It will use the annotation information from input. |
fasta_path |
string containing path to the corresponding fasta file for the modified peptide dataset. |
protein_input |
name of Spectronaut global protein output, which is
as in the same format as |
annotation_protein |
name of annotation file for global protein data, in the same format as above. |
use_unmod_peptides |
If |
intensity |
'PeakArea'(default) uses not normalized peak area. 'NormalizedPeakArea' uses peak area normalized by Spectronaut. Default is NULL |
mod_id |
Character that indicates the modification of interest. Default
is |
fasta_protein_name |
Name of fasta column that matches with protein name
in evidence file. Default is |
remove_other_mods |
Remove peptides which include modfications other
than the one listed in |
filter_with_Qvalue |
TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in EG.Qvalue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose. |
qvalue_cutoff |
Cutoff for EG.Qvalue. Default is 0.01. |
useUniquePeptide |
TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein. |
removeFewMeasurements |
TRUE (default) will remove the features that have 1 or 2 measurements across runs. |
removeProtein_with1Feature |
TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default. |
summaryforMultipleRows |
max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities. |
use_log_file |
logical. If TRUE, information about data processing will be saved to a file. |
append |
logical. If TRUE, information about data processing will be added to an existing log file. |
verbose |
logical. If TRUE, information about data processing wil be printed to the console. |
log_file_path |
character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If 'append = TRUE', has to be a valid path to a file. |
a list of two data.tables named 'PTM' and 'PROTEIN' in the format required by MSstatsPTM.
head(spectronaut_input)
head(spectronaut_annotation)
msstats_input = 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"
)
head(msstats_input$PTM)
head(msstats_input$PROTEIN)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.