Mercurial > repos > eschen42 > mqppep_anova
comparison MaxQuantProcessingScript.R @ 6:922d309640db draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
| author | eschen42 |
|---|---|
| date | Fri, 11 Mar 2022 20:04:05 +0000 |
| parents | d4d531006735 |
| children | d728198f1ba5 |
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| 5:d4d531006735 | 6:922d309640db |
|---|---|
| 519 | 519 |
| 520 # Write quantitative values for debugging purposes | 520 # Write quantitative values for debugging purposes |
| 521 # --- | 521 # --- |
| 522 quant_write <- cbind(metadata_df[, "Sequence window"], quant_data) | 522 quant_write <- cbind(metadata_df[, "Sequence window"], quant_data) |
| 523 colnames(quant_write)[1] <- "Sequence.Window" | 523 colnames(quant_write)[1] <- "Sequence.Window" |
| 524 write.table( | |
| 525 quant_write, | |
| 526 file = quant_file_name, | |
| 527 sep = "\t", | |
| 528 quote = FALSE, | |
| 529 col.names = TRUE, | |
| 530 row.names = FALSE | |
| 531 ) | |
| 524 # ... | 532 # ... |
| 525 | 533 |
| 526 | 534 |
| 527 # Make new data frame containing only Phosphopeptides | 535 # Make new data frame containing only Phosphopeptides |
| 528 # that are to be mapped to quant data (merge_df) | 536 # that are to be mapped to quant data (merge_df) |
| 566 nrow(quant_data_qc) - nrow(quant_data_qc_collapsed) | 574 nrow(quant_data_qc) - nrow(quant_data_qc_collapsed) |
| 567 ) / (2 * nrow(quant_data_qc)) | 575 ) / (2 * nrow(quant_data_qc)) |
| 568 pct_multiphos <- sprintf("%0.1f%s", 100 * pct_multiphos, "%") | 576 pct_multiphos <- sprintf("%0.1f%s", 100 * pct_multiphos, "%") |
| 569 # ... | 577 # ... |
| 570 | 578 |
| 571 write.table( | |
| 572 quant_data_qc_collapsed, | |
| 573 file = quant_file_name, | |
| 574 sep = "\t", | |
| 575 quote = FALSE, | |
| 576 col.names = TRUE, | |
| 577 row.names = FALSE | |
| 578 ) | |
| 579 | 579 |
| 580 # Compute and visualize breakdown of pY, pS, and pT before enrichment filter | 580 # Compute and visualize breakdown of pY, pS, and pT before enrichment filter |
| 581 # --- | 581 # --- |
| 582 py_data <- | 582 py_data <- |
| 583 quant_data_qc_collapsed[ | 583 quant_data_qc_collapsed[ |