Description Usage Arguments Value Author(s)
This function can be used to extract information from the OSW results file obtained from running OpenSwathWorkflow
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | getOSWData_(
oswfile,
run_name = "",
precursor_id = "",
peptide_id = "",
peptide_unmodified = "",
peptide_modified = "",
mod_peptide_id = c("", ""),
mod_residue_position = "",
peak_group_rank_filter = FALSE,
pep_list = "",
mscore_filter = c(SCORE_ = 1),
ipf_filter = "",
ipf_score = FALSE,
ms2_score = TRUE,
decoy_filter = TRUE,
inference_level = "peptide_query"
)
|
oswfile |
A character vector of the absolute path and filename of the osw results file. (Must be .osw format) |
run_name |
A character vector for extraction of a specific run, this should be the same as the file name in the .OSW RUN table. (i.e. run_name='yanliu_I170114_016_PhosNoco4_SW.mzXML.gz', Default: ”) |
precursor_id |
A numeric value for a specific precursor id to extract information for. (Default: ”) |
peptide_id |
A numeric value for a specific peptide id to extract information for. (Default: ”) |
peptide_unmodified |
A string vector indicating a specific unmodified peptide sequence to extract information for. (Default: ”) |
peptide_modified |
A string vector indicating a specific modified peptide sequence to extract information for. (Default: ”) |
mod_peptide_id |
An array of two string vectors indicating a specific modified peptide sequence with both UniMod annotation and actual modification name to extract information for. I.e. c(ANS(Phos)SNSLK, ANS(UniMod:21)SNSLK) (Default: ”) |
mod_residue_position |
A numeric value indicating the position of a modification. (Default: ”) |
peak_group_rank_filter |
A Logical value for filtering OSW results by Peak-Group Rank of 1. (Default: FALSE) |
pep_list |
An arrary of string modified peptide sequences to extract information for. (Default: ”) |
mscore_filter |
A named numeric value to filter results by named q-value. (Default: ”) Options: SCORE_MS2, SCORE_IPF, SCORE_PEPTIDE. Example: c(SCORE_MS2=0.01) |
ipf_filter |
A numeric value to filter results by IPF PEP. (Default: ”) |
ipf_score |
A logical value to extract data using IPF Score results. (Default: FALSE) |
ms2_score |
A logical value to extract data using MS2 Score results. (Default: TRUE) |
decoy_filter |
A logical value to filter decoys out of final results. (Default: TRUE) |
A data.table containing OpenSwath Results information.
Justin Sing https://github.com/singjc
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