Merge pull request #96 from mpi2/dev

v2.0.2: Clean-up

Author: marinak-ebi

Extract details from StatPackets/ExtractPVals.R

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright [yyyy] [name of copyright owner]
+   Copyright [2023-2027] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute.
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

Extract details from StatPackets/ExtractPValsPhenStat.R

@@ -9,4 +9,4 @@ Description: The required package for IMPC ageing pipeline.
 License: LGPL (>= 2)
 Encoding: UTF-8
 LazyData: true
-Imports: RJSONIO, methods, SmoothWin, stringi, base64enc, jsonlite, pingr, foreach, nlme, MASS, base, abind, OpenStats, rlist, DBI, RSQLite, gtools, plyr, robustbase, rlang, RPostgreSQL, data.table, miniparquet, Tmisc
+Imports: RJSONIO, methods, SmoothWin, stringi, base64enc, jsonlite, pingr, foreach, nlme, MASS, base, abind, OpenStats, rlist, DBI, RSQLite, gtools, plyr, robustbase, rlang, RPostgreSQL, data.table, arrow, Tmisc, rwebhdfs

LICENSE

@@ -98,7 +98,6 @@ mainAgeing = function(file = NULL                                    ,
   # Config files
   message0('Loading configuration ...')
   methodmap                      = readConf('MethodMap.conf')
-  equationmap                    = readConf('EquationMap.conf')
   CategoryMap                    = readConf('CategoryMap.conf')
   MergeCategoryParameters        = read.csv(file = file.path(local(), 'MergeParameterList.txt'))
   initial                        = readConf('Initialize.conf')
@@ -672,31 +671,6 @@ mainAgeing = function(file = NULL                                    ,
                       )
                       ###
                       n3.5.2[, depVar] = MergLev$x
-                      ################## Only for Gross Morphology group
-                      # n3.5.2_summary = SummaryStatisticsOriginal(x      = n3.5.2,
-                      #                                          depVar = depVar,
-                      #                                          label  = 'GEL data summary statistics')
-                      # write(
-                      #   paste(
-                      #     c(
-                      #       procedure,
-                      #       parameter,
-                      #       center,
-                      #       strain,
-                      #       zyg,
-                      #       meta,
-                      #       colony,
-                      #       FlatteningTheSummary(n3.5.2_summary, 'GEL data summary statistics')
-                      #     ),
-                      #     sep = '\t',
-                      #     collapse = '\t'
-                      #   ),
-                      #   file = 'summaryStats.tsv',
-                      #   append = TRUE,
-                      #   ncolumns = 10 ^ 4
-                      # )
-                      # return(NULL)
-                      ##################################
                       n3.5.2           = droplevels0(n3.5.2[!is.na(n3.5.2[, depVar]), ])
                       n3.5.2OnlyKO     = subset(n3.5.2,
                                                 n3.5.2$biological_sample_group %in% 'experimental')
@@ -827,8 +801,7 @@ mainAgeing = function(file = NULL                                    ,
                                 data = a@datasetPL
                               ) <= .2 &&
                               EnoughWeightForTheSexGenInteraction(a@datasetPL)         ,
-                            getEquation(var = parameter,
-                                        equationMap = equationmap),
+                            'withWeight',
                             'withoutWeight'
                           )
                         } else{