Append library information to the sampleTable of a qseaSet. Columns are
taken from qseaSet@libraries$file_name, and when available, from
qseaSet@libraries$input_file (prefixed with "input_"). Existing columns
are not duplicated.
addLibraryInformation(qseaSet)A qseaSet object:
addLibraryInformation(): returns the same qseaSet with its
sampleTable augmented by library-level columns.
data(exampleTumourNormal, package = "mesa")
qs <- addLibraryInformation(exampleTumourNormal)
head(qsea::getSampleTable(qs))
#> sample_name group patient type tumour tissue age gender
#> Colon1_N Colon1_N Colon1_N Colon1 NormalColon Normal Colon 80 F
#> Colon1_T Colon1_T Colon1_T Colon1 CRC Tumour Colon 80 F
#> Colon2_N Colon2_N Colon2_N Colon2 NormalColon Normal Colon 67 F
#> Colon2_T Colon2_T Colon2_T Colon2 CRC Tumour Colon 67 F
#> Lung1_N Lung1_N Lung1_N Lung1 NormalLung Normal Lung 64 F
#> Lung1_T Lung1_T Lung1_T Lung1 LUAD Tumour Lung 64 F
#> stage qsea_initial_reads qsea_initial_pairs qsea_initial_r1s
#> Colon1_N <NA> 12692133 6116269 365136
#> Colon1_T III 22233219 10682235 677941
#> Colon2_N <NA> 13665557 6502600 486823
#> Colon2_T IV 17523260 8458460 566689
#> Lung1_N <NA> 24124310 11812879 459951
#> Lung1_T IIA 14777077 7199265 346529
#> qsea_mapq_filtered_pairs qsea_size_filtered_pairs qsea_filtered_r1s
#> Colon1_N 4139702 3973684 245156
#> Colon1_T 8020873 7651545 505870
#> Colon2_N 4495478 4293332 355784
#> Colon2_T 6233320 6093846 375273
#> Lung1_N 8612047 8246187 301844
#> Lung1_T 5571896 5368445 248324
#> total_fragments valid_fragments library_factor offset
#> Colon1_N 4218840 3745354 1.0160834 0.08361333
#> Colon1_T 8157415 7428804 0.9149047 0.11792761
#> Colon2_N 4649116 4195483 0.9700701 0.09683869
#> Colon2_T 6469119 5878535 0.9537051 0.04782413
#> Lung1_N 8548031 7747154 1.0365441 0.08932700
#> Lung1_T 5616769 5208468 1.0701382 0.09292399
#> fragment_median fragment_mean fragment_sd relH GoGe
#> Colon1_N 213 218.0500 92.52174 5.567633 2.554300
#> Colon1_T 205 209.9108 87.52641 4.921130 2.425149
#> Colon2_N 209 213.7803 89.08940 5.399262 2.508576
#> Colon2_T 206 211.7649 83.38018 5.686246 2.529553
#> Lung1_N 170 179.5662 77.17606 4.463002 2.235803
#> Lung1_T 169 178.6148 75.22787 4.406991 2.218343
#> fragments_without_pattern prop_without_pattern initial_reads
#> Colon1_N 580041 0.137 15094748
#> Colon1_T 1288747 0.158 26915464
#> Colon2_N 662701 0.143 16356706
#> Colon2_T 634997 0.098 20229952
#> Lung1_N 1408605 0.165 27826064
#> Lung1_T 915532 0.163 17027817
#> mapped_reads properly_paired_reads contamination_filtered_reads
#> Colon1_N 14500990 13383100 15094748
#> Colon1_T 25724228 23594272 26915464
#> Colon2_N 15582886 14233090 16356706
#> Colon2_T 19406362 18074018 20229952
#> Lung1_N 26718181 25564316 27826064
#> Lung1_T 16328648 15492908 17027817
#> dedup_reads prop_final input_qsea_initial_reads
#> Colon1_N 12709013 0.4962460 4966377
#> Colon1_T 22267932 0.5520101 8396190
#> Colon2_N 13695862 0.5129985 4299845
#> Colon2_T 17532815 0.5811714 7623711
#> Lung1_N 24136005 0.5568272 6856016
#> Lung1_T 14785786 0.6117599 4856759
#> input_qsea_initial_pairs input_qsea_initial_r1s
#> Colon1_N 2414044 121574
#> Colon1_T 4074931 210013
#> Colon2_N 2070056 126214
#> Colon2_T 3705282 193860
#> Lung1_N 3363105 121186
#> Lung1_T 2374289 100993
#> input_qsea_mapq_filtered_pairs input_qsea_size_filtered_pairs
#> Colon1_N 2157040 2022146
#> Colon1_T 3724523 3459159
#> Colon2_N 1883766 1743989
#> Colon2_T 3335781 3154263
#> Lung1_N 2925108 2718410
#> Lung1_T 2088305 1970134
#> input_qsea_filtered_r1s input_total_fragments input_valid_fragments
#> Colon1_N 102865 2125011 2011862
#> Colon1_T 182440 3641599 3443167
#> Colon2_N 110753 1854742 1767031
#> Colon2_T 164778 3319041 3146633
#> Lung1_N 99141 2817551 2667740
#> Lung1_T 83585 2053719 1964050
#> input_library_factor input_offset input_fragment_median
#> Colon1_N NA NA 159
#> Colon1_T NA NA 155
#> Colon2_N NA NA 156
#> Colon2_T NA NA 155
#> Lung1_N NA NA 151
#> Lung1_T NA NA 150
#> input_fragment_mean input_fragment_sd input_relH input_GoGe
#> Colon1_N 170.1683 74.09937 1.506917 1.0294099
#> Colon1_T 164.6657 70.47221 1.446767 1.0094019
#> Colon2_N 165.8846 71.80015 1.608130 1.0823742
#> Colon2_T 163.3088 66.06211 1.474401 1.0054567
#> Lung1_N 157.6033 63.64548 1.437550 0.9970028
#> Lung1_T 157.5332 62.24685 1.481526 1.0093137
#> input_fragments_without_pattern input_prop_without_pattern
#> Colon1_N 564054 0.265
#> Colon1_T 1036999 0.285
#> Colon2_N 485865 0.262
#> Colon2_T 908952 0.274
#> Lung1_N 821455 0.292
#> Lung1_T 569057 0.277
#> input_initial_reads input_mapped_reads input_properly_paired_reads
#> Colon1_N 5432188 5199496 4939766
#> Colon1_T 9253198 8806330 8337544
#> Colon2_N 4794944 4521144 4233954
#> Colon2_T 8310446 7958011 7583394
#> Lung1_N 7495059 7126781 6881304
#> Lung1_T 5295140 5052777 4852748
#> input_contamination_filtered_reads input_dedup_reads input_prop_final
#> Colon1_N 5432188 4969813 0.7407188
#> Colon1_T 9253198 8403358 0.7442112
#> Colon2_N 4794944 4305798 0.7370393
#> Colon2_T 8310446 7628354 0.7572718
#> Lung1_N 7495059 6859166 0.7118663
#> Lung1_T 5295140 4859263 0.7418312