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UCLouvain-CBIO / scp

Single cell proteomics data processing
https://uclouvain-cbio.github.io/scp/index.html
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Vignette/data import/readSCP #21

Closed edemmott closed 3 years ago

edemmott commented 3 years ago

The maxquant evidence file used for the vignette appears to deviate from the default maxquant. To get it to behave I needed to rename a number of columns:

names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.1"] <- "RI1" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.2"] <- "RI2" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.3"] <- "RI3" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.4"] <- "RI4" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.5"] <- "RI5" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.6"] <- "RI6" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.7"] <- "RI7" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.8"] <- "RI8" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.9"] <- "RI9" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.10"] <- "RI10" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.11"] <- "RI11" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.12"] <- "RI12" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.13"] <- "RI13" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.14"] <- "RI14" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.15"] <- "RI15" names(mqSCPdata)[names(mqSCPdata) == "Reporter.intensity.corrected.16"] <- "RI16" names(mqSCPdata)[names(mqSCPdata) == "Raw.file"] <- "Set"

cvanderaa commented 3 years ago

Hello @edemmott , Thank you very much for your feedback. I'm not sure to understand whether you need to rename the column names to run the vignette/example (should not be the case) or to run on your own data (then indeed renaming might be required). Anyway, I think you raise a good point, that is the example data should contain the default MaxQuant column names. I'll adapt this soon. Best, Chris

cvanderaa commented 3 years ago

I adapted the example data, the documentation and vignette. I hope this improvement is in line with the issue raised.

cvanderaa commented 3 years ago

I will close this issue because we will create a new vignette to better describe how to import data using scp (see issue #23 ). Any suggestions there are welcome!