missed cleavages from evidence.txt #104
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cbielow
reviewed
Jul 12, 2021
cbielow
reviewed
Jul 12, 2021
cbielow
reviewed
Jul 12, 2021
cbielow
reviewed
Jul 12, 2021
cbielow
reviewed
Jul 13, 2021
R/createReport.R
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| @@ -515,7 +516,7 @@ createReport = function(txt_folder = NULL, mztab_file = NULL, yaml_obj = list(), | |||
| lst_qcMetrics[["qcMetric_EVD_MissingValues"]]$setData(df_evd) | |||
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| ## trim down to the absolute required (we need to identify contaminants in MSMS.txt later on) | |||
| if (!DEBUG_PTXQC) df_evd = df_evd[, c("id", "contaminant")] | |||
| if (!DEBUG_PTXQC) df_evd = df_evd[, c("id", "contaminant", "fc.raw.file", "sequence", "missed.cleavages")] | |||
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unfortunately, this will throw an error if missed.cleavages is missing.
However, if (!DEBUG_PTXQC) df_evd = df_evd[, names(df_evd) %in% c("id", "contaminant", "fc.raw.file", "sequence", "missed.cleavages")] should work.
cbielow
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missed cleavages metric can be computed from evidence.txt (for more recent versions of MaxQuant) if msms.txt is not provided