Retrieve normalised counts of MAC-seq data
Source:R/compute_normalised_counts.R
compute_normalised_counts.RdThis function retrieves counts from a number of methods that are available for normalisation, with the default of limma-voomLmFit.
Usage
compute_normalised_counts(
data = NULL,
method = NULL,
batch = NULL,
k = NULL,
spikes = NULL,
max_counts = NULL
)Arguments
- data
A tidyseurat object merged with metadata. Must contain columns "Well_ID", "Row", "Column"
- method
One of "raw", "logNorm", "cpm", "clr", "SCT", "DESeq2", "edgeR", "RUVg", "RUVs", "RUVr", "limma_voom"
- batch
Either empty, a single value, or a vector corresponding to the number of samples
- k
Parameter k for RUVSeq methods, check RUVSeq tutorial
- spikes
List of genes to use as spike controls
- max_counts
Maximum count for a gene across all samples
Examples
data(mini_mac)
compute_normalised_counts(mini_mac)
#> AACAGGCAAT AACCAGCCAG AACCAGTTGA AACCGGCGTA AACCTAGTCC
#> NAMPT 13.66997 14.260025 14.44157 13.909156 13.56072
#> ENSG00000278869 12.08500 9.867707 10.19365 9.661228 10.75337
#> CABP7-DT 12.08500 9.867707 10.19365 9.661228 10.75337
#> AACTCTACAC AACTGTGTCA AAGATGTCCA AAGCATATGG AAGCTCACCT
#> NAMPT 14.045187 13.47592 14.06636 13.843252 14.546433
#> ENSG00000278869 9.797259 10.30599 10.60693 9.936361 9.902577
#> CABP7-DT 9.797259 10.30599 10.60693 9.936361 9.902577
#> AAGGCATGCG AAGTTCCTTG AATACCGGTA AATCCATCTG AATCGTCCGC
#> NAMPT 14.09024 14.236369 12.65557 14.390264 14.19258
#> ENSG00000278869 10.38980 9.988441 10.33364 9.866702 10.28569
#> CABP7-DT 10.38980 9.988441 10.33364 9.866702 10.28569
#> AATGACCTTC AATGAGAGCA AATGTCAGTG AATTAGGCCG AATTGCGATG
#> NAMPT 14.13132 13.84006 14.23717 14.78534 14.04032
#> ENSG00000278869 10.22443 10.38063 10.14970 10.26178 10.33988
#> CABP7-DT 10.22443 10.38063 10.14970 10.26178 10.33988
#> ACAACAGTCG ACAACCATAC ACAACGGAGC ACAAGCGCGA ACACAATCTC
#> NAMPT 14.22746 13.67637 13.29803 13.91466 14.152842
#> ENSG00000278869 10.32057 11.80190 10.49068 10.21422 9.904915
#> CABP7-DT 10.32057 10.21694 10.49068 10.21422 9.904915
#> ACACAGTGAA ACACCGAATT ACACGCAGTA ACACGGTCCT ACACTTGCTG
#> NAMPT 13.77927 10.32576 13.33117 14.389019 12.62004
#> ENSG00000278869 10.97192 10.32576 10.16124 9.996701 10.29811
#> CABP7-DT 10.97192 10.32576 10.16124 9.996701 10.29811
#> ACAGTGCCAA ACATGTGTGC ACCAGGACCA ACCATAACAC ACCGAACCGT
#> NAMPT 12.62198 14.458157 14.78237 13.93570 13.72066
#> ENSG00000278869 11.03701 9.934595 10.13852 10.23526 10.02022
#> CABP7-DT 11.03701 9.934595 10.13852 10.23526 10.02022
#> ACCGAGAGTC ACCGGTACAG ACCGTACTTC ACCTCCGACA ACCTCTCTCC
#> NAMPT 13.58220 13.33547 13.61461 13.80380 13.68839
#> ENSG00000278869 10.41227 10.52812 10.44468 10.34436 10.22896
#> CABP7-DT 10.41227 10.52812 10.44468 10.34436 10.22896
#> ACCTGTCCGA ACGAATGACA ACGCTGGATA ACGTAGGCAC ACGTGCTGAT
#> NAMPT 13.90623 13.378382 14.08211 13.58088 14.05796
#> ENSG00000278869 10.44680 9.918951 10.38167 10.41096 10.35752
#> CABP7-DT 10.44680 9.918951 10.38167 10.41096 10.35752
#> ACTCCAAGCC ACTGGCGCAT ACTGGCTTCC ACTTAACTGC ACTTCATCAC
#> NAMPT 14.32798 14.19152 13.23157 14.524254 13.89201
#> ENSG00000278869 10.08005 10.10406 10.90964 9.769367 10.19157
#> CABP7-DT 10.08005 10.10406 10.90964 9.769367 10.19157
#> ACTTCGTTGA ACTTCTCCTG ACTTGAGGAA ACTTGTAAGG AGAACCACGG
#> NAMPT 13.99649 12.88988 13.439895 12.75603 14.19658
#> ENSG00000278869 10.08960 10.56795 9.980464 10.43410 10.49614
#> CABP7-DT 10.08960 10.56795 9.980464 10.43410 10.49614
#> AGAAGCAATC AGACCGTTAT AGACTAGCAT AGAGATGCAG AGAGCTTACA
#> NAMPT 14.22715 14.205986 13.93058 13.96693 14.25161
#> ENSG00000278869 10.13969 9.958058 10.76066 10.26649 10.00369
#> CABP7-DT 10.13969 9.958058 10.76066 10.26649 10.00369
#> AGAGTGTAAC AGAGTTCTGC AGATAGTGCT AGCAATGCGC AGCATGTCAT
#> NAMPT 13.66390 14.53844 13.406628 13.95211 14.20371
#> ENSG00000278869 10.20447 10.63155 9.947196 10.04522 10.29682
#> CABP7-DT 10.20447 10.63155 9.947196 10.04522 10.29682
#> AGCCACTAGC AGCCAGAATA AGCCAGCTCT AGCGATAACG AGCTATTCCA
#> NAMPT 14.39311 14.045900 13.896092 13.11280 14.355971
#> ENSG00000278869 10.14518 9.958437 9.989202 10.30545 9.963654
#> CABP7-DT 10.14518 9.958437 9.989202 10.30545 9.963654
#> AGGCGTCTGT AGGTCACCAA AGTAACTCAC AGTAAGCGTT AGTCCACGTA
#> NAMPT 14.59436 13.67424 13.90536 14.07932 14.083966
#> ENSG00000278869 10.20205 10.21480 10.20492 10.37888 12.318431
#> CABP7-DT 10.20205 10.21480 10.20492 10.37888 9.996503
#> AGTCTCGGCA AGTCTGTACG AGTGCAATGT ATAACGCCTC ATAAGAGGTC
#> NAMPT 14.48354 13.37684 13.81293 14.11309 14.19242
#> ENSG00000278869 10.39608 10.20691 10.35350 9.86516 10.49198
#> CABP7-DT 10.39608 10.20691 10.35350 9.86516 10.49198
#> ATAAGGTGCA ATACACGACA ATACCTCCGG ATAGCAGTGC ATAGGCCATT
#> NAMPT 13.59311 14.15351 13.380159 12.64341 13.91116
#> ENSG00000278869 10.13368 10.24661 9.920727 10.32148 10.00427
#> CABP7-DT 10.13368 10.24661 9.920727 10.32148 10.00427
#> ATATCCGCAT ATCAGCACTT ATCAGCGAGG ATCCAATACG ATCCGCTGTG
#> NAMPT 13.20469 14.30919 14.28599 13.835359 13.51872
#> ENSG00000278869 10.39733 10.40230 10.37910 9.928468 10.34879
#> CABP7-DT 10.39733 10.40230 10.37910 9.928468 10.34879
#> ATCCGTCCAT ATCGACGGCT ATCGCGATTA ATCGGTAGGC ATCTAAGGAG
#> NAMPT 13.655788 14.27063 13.72080 13.77757 14.418766
#> ENSG00000278869 9.955348 10.36374 10.02036 10.07713 9.895204
#> CABP7-DT 9.955348 10.36374 10.02036 10.07713 9.895204
#> ATGACGGTAA ATGACTCAGT ATGCGGACTG ATGGTCTTAG ATGTGGAAGC
#> NAMPT 14.47485 13.83903 14.708160 13.34782 13.85146
#> ENSG00000278869 10.22693 9.93214 9.850179 10.54047 10.39203
#> CABP7-DT 10.22693 9.93214 9.850179 10.54047 10.39203
#> ATTATCGGAC ATTCGGAACA CAACAATCCA CAAGAAGCAT CAAGATGAGG
#> NAMPT 14.38714 12.83998 14.14760 13.75141 13.759497
#> ENSG00000278869 10.29968 10.51805 10.24071 10.29198 9.852606
#> CABP7-DT 10.29968 10.51805 10.24071 10.29198 9.852606
#> CAAGCCAACG CAAGTGGATC CACAGTTCAT CACGAGTCTG CACGCTCCAA
#> NAMPT 12.79278 14.13392 14.03263 14.62014 14.13498
#> ENSG00000278869 11.20782 9.88599 10.33219 10.09658 10.43454
#> CABP7-DT 11.20782 9.88599 10.33219 10.09658 10.43454
#> CACTGAGCAC CAGATCAATG CAGTGCTCTT CAGTTAAGCA CATAGCTATC
#> NAMPT 14.35395 13.84167 14.23031 13.81527 13.89587
#> ENSG00000278869 10.10602 10.38224 9.98238 10.35584 10.19543
#> CABP7-DT 10.10602 10.38224 9.98238 10.35584 10.19543
#> CATCACCACC CATGTACGCC CATTACACTG CATTCGACGA CCAACTATGG
#> NAMPT 14.75381 13.92909 14.08192 13.895667 12.88798
#> ENSG00000278869 10.50588 10.02220 10.38148 9.988777 10.56605
#> CABP7-DT 10.50588 10.02220 10.38148 9.988777 10.56605
#> CCAAGGAGTT CCAATTGTTC CCACAAGTGC CCAGCTTAGT CCATAACTTG
#> NAMPT 14.453685 14.38994 14.464874 14.09772 13.624526
#> ENSG00000278869 9.809829 10.30248 9.941312 10.92780 9.717635
#> CABP7-DT 9.809829 10.30248 9.941312 10.92780 9.717635
#> CCATAGATCA CCGAACAAGC CCGAAGACCT CCGAATAGTG CCGACTTCTC
#> NAMPT 14.192856 13.64834 14.32621 14.43232 14.71488
#> ENSG00000278869 9.800538 12.06338 10.62577 10.04000 10.32257
#> CABP7-DT 9.800538 10.47842 10.62577 10.04000 10.32257
#> CCGATCCACT CCGATGATAC CCGCGTTATG CCGCTAGCTT CCGGAGTATC
#> NAMPT 13.59321 14.04795 13.86349 14.13613 14.81530
#> ENSG00000278869 12.00824 10.58852 10.16305 10.22924 10.06041
#> CABP7-DT 10.42328 10.58852 10.16305 10.22924 10.06041
#> CCGGCCAATT CCGGTCTCTA CCGTACGATG CCGTCAGAAC CCTAGACACG
#> NAMPT 13.99348 14.58924 13.39697 14.166851 13.85250
#> ENSG00000278869 10.29304 10.06568 10.58962 9.774533 10.15206
#> CABP7-DT 10.29304 10.06568 10.58962 9.774533 10.15206
#> CCTAGTTGAG CCTATTCTGT CCTCAACCGA CCTCCATAAG CCTGATGCCA
#> NAMPT 14.44526 14.80778 14.62671 14.11069 13.94918
#> ENSG00000278869 10.19734 10.55986 10.23439 10.20380 9.86172
#> CABP7-DT 10.19734 10.55986 10.23439 10.20380 9.86172
#> CCTGCAATAC CCTTGTATTC CGAGATCTCT CGAGGAACAA CGATAACCGC
#> NAMPT 13.49066 13.96961 13.38090 14.73580 14.19375
#> ENSG00000278869 10.32073 10.06272 10.57355 11.67691 10.28686
#> CABP7-DT 10.32073 10.06272 10.57355 10.09195 10.28686
#> CGATCCTGTG CGCCAACCAT CGCCAGTGTT CGCGGATTCA CGCTTCTTGG
#> NAMPT 14.069789 13.76564 14.45898 13.696850 14.54643
#> ENSG00000278869 9.982326 11.44371 10.06667 9.996411 10.29851
#> CABP7-DT 9.982326 11.44371 10.06667 9.996411 10.29851
#> CGGAATACAC CGGAGATTGG CGGAGCTCAA CGGATCGGTA CGGATTCTAG
#> NAMPT 14.10723 14.45082 13.96841 14.499409 13.11294
#> ENSG00000278869 10.40679 10.36335 10.26797 9.855552 10.30559
#> CABP7-DT 10.40679 10.36335 10.26797 9.855552 10.30559
#> CGGCAACTTA CGGCTCATCA CGGTCGTATT CGGTGACATC CGTAACGGAT
#> NAMPT 12.82179 14.11113 14.16814 12.88258 14.34739
#> ENSG00000278869 10.01443 10.41069 10.08067 10.56065 10.09946
#> CABP7-DT 10.01443 10.41069 10.08067 10.56065 10.09946
#> CGTAAGATTC CGTACTGTAA CGTAGAAGAC CGTCCTAGGA CGTCGGCAAT
#> NAMPT 13.64759 13.57998 14.45721 13.888355 13.45407
#> ENSG00000278869 10.18816 10.12055 10.36975 9.981465 10.28415
#> CABP7-DT 10.18816 10.12055 10.36975 9.981465 10.28415
#> CGTGAGTTAT CGTGTCAAGC CTAACTTCAG CTAATAGCGT CTACACCAGG
#> NAMPT 14.21134 12.86255 14.389230 13.88852 14.203103
#> ENSG00000278869 10.12387 10.54062 9.996913 12.01405 9.955175
#> CABP7-DT 10.12387 10.54062 9.996913 10.42908 9.955175
#> CTAGCACAAT CTATGAACGG CTCAAGGACC CTCACCTGTC CTCCTATTGT
#> NAMPT 13.973762 14.283509 14.02354 14.41938 13.524988
#> ENSG00000278869 9.886299 9.891191 10.32310 10.02706 9.824548
#> CABP7-DT 9.886299 9.891191 10.32310 10.02706 9.824548
#> CTCGCAACGT CTGGATTGAC CTGTCTGTGT CTTATGTTGC CTTCATATCG
#> NAMPT 13.903956 14.25770 13.56746 14.12393 13.892189
#> ENSG00000278869 9.997065 10.17024 10.39753 10.21704 9.804727
#> CABP7-DT 9.997065 10.17024 10.39753 10.21704 9.804727
#> CTTGCTGACG CTTGGATCTT GAAGAGTTCT GAAGGATTAG GAATCGAGCC
#> NAMPT 13.53461 14.10169 14.60146 13.85138 13.17640
#> ENSG00000278869 10.72725 10.01423 10.20914 10.15094 10.36904
#> CABP7-DT 10.72725 10.01423 10.20914 10.15094 10.36904
#> GAATCTTCTC GAATTACGGC GACCATCTAA GACGACCACA GAGAACGAAG
#> NAMPT 13.20838 14.26026 14.169591 14.15530 14.32893
#> ENSG00000278869 10.03845 10.35336 9.921664 10.45486 11.66597
#> CABP7-DT 10.03845 10.35336 9.921664 10.45486 10.08101
#> GAGACAAGGC GAGACATCTT GAGCGAGTCA GAGTAGACCA GATACGCTTA
#> NAMPT 14.17458 13.31867 12.82448 13.94739 12.69029
#> ENSG00000278869 11.85265 10.14874 10.50256 10.04050 11.10533
#> CABP7-DT 10.26769 10.14874 10.50256 10.04050 11.10533
#> GATAGACTGT GATAGAGGCG GATAGGTCAA GATATCAGGA GATCTCATTC
#> NAMPT 12.95078 13.50194 14.17048 13.76605 13.58436
#> ENSG00000278869 10.62885 10.69458 10.08301 10.30662 10.12493
#> CABP7-DT 10.62885 10.69458 10.08301 10.30662 10.12493
#> GATCTGGTCG GATGAGTGAC GATGGATACA GATGTGACAG GATTGCACGC
#> NAMPT 13.44772 14.225836 14.69629 13.99576 10.88166
#> ENSG00000278869 10.27780 9.977908 10.17273 10.08887 10.88166
#> CABP7-DT 10.27780 9.977908 10.17273 10.08887 10.88166
#> GCACACTATA GCACTGCGTT GCACTTAATC GCAGGAGATG GCAGTACTGG
#> NAMPT 14.06808 13.50116 13.875953 13.89685 14.519691
#> ENSG00000278869 10.36764 10.33124 9.969063 10.43742 9.996129
#> CABP7-DT 10.36764 10.33124 9.969063 10.43742 9.996129
#> GCATATGAGT GCATCCGATC GCCAAGTACA GCCACGATTC GCCATAGGTT
#> NAMPT 14.49169 14.25239 13.43202 14.41545 13.66035
#> ENSG00000278869 10.24377 10.00446 10.26210 10.02313 10.20092
#> CABP7-DT 10.24377 10.00446 10.26210 10.02313 10.20092
#> GCCATATCGA GCCGTCAATA GCCTGGACAT GCGTAATTAC GCTATTATCC
#> NAMPT 14.140329 13.76553 14.089849 13.80946 13.486204
#> ENSG00000278869 9.892401 10.30610 11.426884 10.35003 9.785764
#> CABP7-DT 9.892401 10.30610 9.841921 10.35003 9.785764
#> GCTCAGTAAT GCTGCTTATA GGAATAAGCA GGACGATGCT GGCATCGTGA
#> NAMPT 13.63412 13.83237 14.28263 12.39894 13.61543
#> ENSG00000278869 10.82677 10.13193 10.37574 10.07701 10.44550
#> CABP7-DT 10.82677 10.13193 10.37574 10.07701 10.44550
#> GGCATTATTG GGCCGAGATT GGCGCTATAA GGCGTTAAGT GGCTATTGAT
#> NAMPT 14.04289 13.62700 14.160058 13.67315 13.21275
#> ENSG00000278869 10.13600 10.16757 11.497093 10.21372 10.04282
#> CABP7-DT 10.13600 10.16757 9.912131 10.21372 10.04282
#> GGCTGCTACT GGTAATGTGT GGTGTTCACC GGTTCACTGG GTAACCAGTA
#> NAMPT 13.78544 14.27067 14.54249 14.02450 13.62434
#> ENSG00000278869 10.32600 10.02274 10.15017 10.56507 10.16491
#> CABP7-DT 10.32600 10.02274 10.15017 10.56507 10.16491
#> GTAACCTTGG GTAAGAACCT GTAAGGCTCC GTAATCCACG GTATTGTGGA
#> NAMPT 13.73078 13.77462 13.65875 13.50599 14.16883
#> ENSG00000278869 10.03034 10.07418 10.19932 10.04656 10.08136
#> CABP7-DT 10.03034 10.07418 10.19932 10.04656 10.08136
#> GTCCGCATCA GTCCTTCGGT GTCGCTCTCT GTCGGTGACA GTCTCGAGTG
#> NAMPT 14.12045 15.05770 13.97768 13.309835 13.63661
#> ENSG00000278869 10.42001 10.19971 10.27725 9.850403 10.46669
#> CABP7-DT 10.42001 10.19971 10.27725 9.850403 10.46669
#> GTCTCTTAAG GTCTTCCGAG GTGACTATAC GTGGTTAATG GTGTGCCTGT
#> NAMPT 14.31048 13.69240 13.944329 14.18121 13.72460
#> ENSG00000278869 10.40359 10.52248 9.856866 10.27432 10.26517
#> CABP7-DT 10.40359 10.52248 9.856866 10.27432 10.26517
#> GTGTGTGTCC GTTCATTGCC GTTCCGGTGA GTTCGTCGAA GTTGAATTGG
#> NAMPT 14.26303 14.22101 13.25959 13.86624 13.57186
#> ENSG00000278869 10.17557 10.13355 10.45223 9.95935 10.40194
#> CABP7-DT 10.17557 10.13355 10.45223 9.95935 10.40194
#> GTTGATCCGC GTTGTATGCT TAACCGTAGC TAACGTCGAT TAAGGTACGG
#> NAMPT 12.701573 14.043267 14.33462 14.06657 14.598048
#> ENSG00000278869 9.894218 9.955805 10.08669 10.15967 9.843161
#> CABP7-DT 9.894218 9.955805 10.08669 10.15967 9.843161
#> TACTACCGCC TAGCGCCAAC TAGGTTGCAA TAGTAGTCTC TAGTCCGCTG
#> NAMPT 14.569266 13.52407 13.96091 14.282132 13.62775
#> ENSG00000278869 9.925409 10.71671 10.26047 9.889814 10.45783
#> CABP7-DT 9.925409 10.71671 10.26047 9.889814 10.45783
#> TAGTGGAACT TATCATGCAG TATCGTTACG TCAAGTGCAG TCACAGATAC
#> NAMPT 12.60432 13.34823 13.97041 13.79348 14.55655
#> ENSG00000278869 10.28239 10.17831 10.06351 10.33404 10.03298
#> CABP7-DT 10.28239 10.17831 10.06351 10.33404 10.03298
#> TCACCGCCTA TCACGCCACT TCACGTTGGC TCATTGTCCA TCCACACTAG
#> NAMPT 13.97246 13.98971 13.50309 14.64208 13.02373
#> ENSG00000278869 10.27202 10.08282 10.33316 10.11852 10.21638
#> CABP7-DT 10.27202 10.08282 10.33316 10.11852 10.21638
#> TCCACGGTCA TCCACTCGCT TCCGACTAAC TCCGTTATCT TCCTAAGAGA
#> NAMPT 14.64278 12.33585 14.71994 14.10845 14.34250
#> ENSG00000278869 10.11922 10.75088 10.19638 10.20156 10.43561
#> CABP7-DT 10.11922 10.75088 10.19638 10.20156 10.43561
#> TCCTCTAGTA TCGAAGCATT TCGAGAGAGC TCGCACTTGA TCGCCTACTG
#> NAMPT 13.62554 13.77115 11.95421 14.833341 12.67466
#> ENSG00000278869 10.81819 10.60123 10.36925 9.879145 10.35273
#> CABP7-DT 10.81819 10.60123 10.36925 9.879145 10.35273
#> TCGCGTAGCA TCGGCGTTAA TCTACATCCG TCTCTCCTAT TGAAGAAGGT
#> NAMPT 13.52208 14.43634 14.58437 14.92699 14.93352
#> ENSG00000278869 10.35215 10.04402 10.49691 9.97279 10.28966
#> CABP7-DT 10.35215 10.04402 10.49691 9.97279 10.28966
#> TGAGCGTTCC TGAGTACGTA TGGAATGGAG TGTCATTCGC TGTGCTTCAG
#> NAMPT 14.47326 13.31961 13.66720 14.58681 14.197272
#> ENSG00000278869 10.08094 10.51225 10.20777 10.49935 11.534307
#> CABP7-DT 10.08094 10.51225 10.20777 10.49935 9.949344
#> TGTTCAGGAT TTACACACGT TTACTGTGAC TTATGCCGCG TTCACGGAAG
#> NAMPT 13.63357 14.565143 14.50972 14.45371 14.27686
#> ENSG00000278869 10.17414 9.707162 10.60283 10.06139 10.36997
#> CABP7-DT 10.17414 9.707162 10.60283 10.06139 10.36997
#> TTCGAGTGAT TTCTGTACCT TTGGTAACAG
#> NAMPT 14.59300 14.17005 14.297836
#> ENSG00000278869 10.20068 10.71062 9.905519
#> CABP7-DT 10.20068 10.71062 9.905519
#> [ reached getOption("max.print") -- omitted 497 rows ]