modified unit tests to match altered functions in DIMS/peak_finding and /collect_filled

Author: mraves2

DIMS/tests/testthat/fixtures/test_peakgroup_list.txt

@@ -1,5 +1,5 @@
-"mzmed.pgrp"	"nrsamples"	"C101.1"	"C102.1"	"P2.1"	"P3.1"	"assi_HMDB"	"all_hmdb_names"	"iso_HMDB"	"HMDB_code"	"all_hmdb_ids"	"sec_hmdb_ids"	"theormz_HMDB"	"avg.int"	"avg.ctrls"	"sd.ctrls"	"C101.1_Zscore"	"C102.1_Zscore"	"P2.1_Zscore"	"P3.1_Zscore"	"ppmdev"
-"1"	300.199680958642	0.451108327135444	1000	5000	10000	50000	"A"	"A;X"	NA	"HMDB1234567"	"HMDB1234567;HMDB1234567"	NA	300.1996476	16500	3000	2828.42712474619	9000	13000	90000	130000	0.111112214857712
-"2"	300.000315890415	0.498603057814762	2000	6000	20000	60000	"B"	"B;Y"	NA	"HMDB1234567_1"	"HMDB1234567_1;HMDB1234567_1"	NA	300.00017417	22000	4000	2828.42712474619	10000	14000	1e+05	140000	0.473299680976197
-"3"	300.254185894039	0.589562055887654	3000	7000	30000	70000	"C"	"C;Z"	NA	"HMDB1234567_2"	"HMDB1234567_2;HMDB1234567_2"	NA	300.25413357	27500	5000	2828.42712474619	11000	15000	110000	150000	0.17426158930175
-"4"	300.755745105678	0.277923040557653	4000	8000	40000	80000	"D"	"D;V"	NA	"HMDB1234567_7"	"HMDB1234567_7;HMDB1234567_7"	NA	300.75568892	33000	6000	2828.42712474619	12000	16000	120000	160000	0.186787674436346
+"mzmed.pgrp"	"nrsamples"	"C101.1"	"C102.1"	"P2.1"	"P3.1"	"assi_HMDB"	"all_hmdb_names"	"iso_HMDB"	"HMDB_code"	"all_hmdb_ids"	"sec_hmdb_ids"	"theormz_HMDB"	"ppmdev"	"avg.int"	"avg.ctrls"	"sd.ctrls"	"C101.1_Zscore"	"C102.1_Zscore"	"P2.1_Zscore"	"P3.1_Zscore"
+"1"	300.199680958642	0.451108327135444	1000	5000	10000	50000	"A"	"A;X"	NA	"HMDB1234567"	"HMDB1234567;HMDB1234567"	NA	300.1996476	0.111112214857712	16500	3000	2828.42712474619	9000	13000	90000	130000
+"2"	300.000315890415	0.498603057814762	2000	6000	20000	60000	"B"	"B;Y"	NA	"HMDB1234567_1"	"HMDB1234567_1;HMDB1234567_1"	NA	300.00017417	0.473299680976197	22000	4000	2828.42712474619	10000	14000	1e+05	140000
+"3"	300.254185894039	0.589562055887654	3000	7000	30000	70000	"C"	"C;Z"	NA	"HMDB1234567_2"	"HMDB1234567_2;HMDB1234567_2"	NA	300.25413357	0.17426158930175	27500	5000	2828.42712474619	11000	15000	110000	150000
+"4"	300.755745105678	0.277923040557653	4000	8000	40000	80000	"D"	"D;V"	NA	"HMDB1234567_7"	"HMDB1234567_7;HMDB1234567_7"	NA	300.75568892	0.186787674436346	33000	6000	2828.42712474619	12000	16000	120000	160000

DIMS/tests/testthat/test_collect_filled.R

@@ -65,7 +65,7 @@ testthat::test_that("columns in peak group list are corretly sorted", {
   # original order of columns
   original_column_order <- colnames(test_peakgroup_list)
   # after ordering, column names should be re-ordered
-  test_column_order <- original_column_order[c(1, 2, 7:14, 21, 3:6, 15:20)]
+  test_column_order <- original_column_order[c(1, 2, 7:15, 3:6, 16:21)]
 
   expect_identical(colnames(order_columns_peakgrouplist(test_peakgroup_list)), test_column_order)
 

DIMS/tests/testthat/test_peak_finding_functions.R

@@ -31,7 +31,7 @@ test_that("regions of interest are correctly found for two peaks", {
                                              int = test_ints_range))
 
   # expected output
-  expected_output <- as.data.frame(matrix(c(1, 8, 8, 20, 8, 13), nrow = 2, ncol = 3))
+  expected_output <- as.data.frame(matrix(c(1, 8, 8, 21, 7, 13), nrow = 2, ncol = 3))
   colnames(expected_output) <- c("from", "to", "length")
   rownames(expected_output) <- as.character(c(1, 2))