releasing version 1.0.10

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: PTXQC
 Type: Package
 Title: Quality Report Generation for MaxQuant and mzTab Results
-Version: 1.0.9
-Date: 2021-01-29
+Version: 1.0.10
+Date: 2021-05-29
 Author: Chris Bielow [aut, cre],
   Juliane Schmachtenberg [ctb],
   Swenja Wagner [ctb],

NEWS

@@ -7,6 +7,12 @@ Versions uploaded to CRAN are marked with [CRAN].
 #########   CHANGELOG  ##########
 #################################
 
+[CRAN] v1.0.10 -- 2021/05/29
+  - [FEATURE] detect if MaxQuant was run with wrong decimal separator (non UK/US locale) (issue #98)
+  - [FIX] issue #97 Revive missing MBR metrics (introduced in PTXQC 1.0.9)
+  - [FIX] issue #101 Restore full Parameter list showing MaxQuant parameters
+  - [FIX] issue #102 Decoy distribution not shown in MS/MS mass error plot
+
 [CRAN] v1.0.9 -- 2021/01/29
   - [FEATURE] allow redirecting console output to file (#94)
   - [FIX] reduce ggplot warnings

R/qcMetric_EVD.R

@@ -816,7 +816,7 @@ Heatmap score: none.
         RTalignmentTree(df_evd[(df_evd$type %in% c("MULTI-MSMS")), 
                                c("calibrated.retention.time", "fc.raw.file", col_fraction, "modified.sequence", "charge")],
                         col_fraction = col_fraction)
-      
+
       ## MBR: additional evidence by matching MS1 by AMT across files
       if (any(df_evd$is.transferred)) {
         ## gain for each raw file: absolute gain, and percent gain

README.md

@@ -9,8 +9,10 @@ PTXQC
 
 ### Latest changes / ChangeLog
 
-  - v1.00.09 - Jan 2021: output logging to external file (#94); mzQC support (partial); less warnings;
-  - v1.00.08 - Dec 2020: fix issues with two metrics (#90, #91)
+
+  - v1.00.10 - May 2021: detect non UK/US locale (https://github.com/cbielow/PTXQC/pull/99); Revive missing MBR metrics (https://github.com/cbielow/PTXQC/issues/97); restore full Parameter list (showing MaxQuant parameters (https://github.com/cbielow/PTXQC/issues/101); decoy distribution in MS/MS mass error plot restored (https://github.com/cbielow/PTXQC/issues/102)
+  - v1.00.09 - Jan 2021: output logging to external file (https://github.com/cbielow/PTXQC/issues/94); mzQC support (partial); less warnings;
+  - v1.00.08 - Dec 2020: fix issues with two metrics (https://github.com/cbielow/PTXQC/issues/90, https://github.com/cbielow/PTXQC/issues/91)
   - v1.00.07 - Nov 2020: fix issues with creating intermediate Rplots.pdf
   - v1.00.05 - Jun 2020: mzTab fixes introduced in v1.0.4
 
@@ -39,6 +41,7 @@ DOI: [10.1021/acs.jproteome.5b00780][JPR_paper]
     - Match-between-runs performance
   - easy usage ([Windows OS only] `drag'n'drop` your `txt output folder` onto a `batch file`)
     - 10 min [Installation](#installation)
+  - MaxQuant locale check, i.e. dot as decimal separator (since PTXQC 1.0.10; see https://github.com/cbielow/PTXQC/pull/99 for details)
   - Html/PDF report will be generated within your MaxQuant-txt folder or next to the mzTab file
   - optional configuration file *in YAML format* for generation of shorter/customized reports
 

inst/examples/README.md

@@ -41,5 +41,5 @@ See the package vignettes for documentation on how to create and customize a rep
   [4]: https://github.com/cbielow/PTXQC/blob/master/vignettes/PTXQC-Basic_Guide_for_R_users.Rmd
   [5]: https://github.com/cbielow/PTXQC/blob/master/vignettes/PTXQC-DragNDrop.Rmd
   [JPR_paper]: https://doi.org/10.1021/acs.jproteome.5b00780
-  [example_html]: http://htmlpreview.github.io/?https://github.com/cbielow/PTXQC/blob/master/inst/examples/report_v1.0.0__txt_5files_withMatch-100min.html
-  [example_pdf]: report_v1.0.0__txt_5files_withMatch-100min.pdf
+  [example_html]: http://htmlpreview.github.io/?https://github.com/cbielow/PTXQC/blob/master/inst/examples/report_v1.0.10__txt_5files_withMatch-100min.html
+  [example_pdf]: report_v1.0.10__txt_5files_withMatch-100min.pdf