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,
num_cores = 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", "limma_trend", "zinb"
- batch
Either empty, a single value, or a vector corresponding to the number of samples
- k
Parameter k for RUVSeq and zinb methods
- spikes
List of genes to use as spike controls
- max_counts
Maximum count for a gene across all samples
- num_cores
Number of cores
Examples
data(mini_mac)
compute_normalised_counts(mini_mac)
#> AACAGGCAAT AACCAGCCAG AACCAGTTGA AACCGGCGTA AACCTAGTCC
#> NAMPT 13.7 14.26 14.4 13.91 13.6
#> ENSG00000278869 12.1 9.87 10.2 9.66 10.8
#> CABP7-DT 12.1 9.87 10.2 9.66 10.8
#> AACTCTACAC AACTGTGTCA AAGATGTCCA AAGCATATGG AAGCTCACCT
#> NAMPT 14.0 13.5 14.1 13.84 14.5
#> ENSG00000278869 9.8 10.3 10.6 9.94 9.9
#> CABP7-DT 9.8 10.3 10.6 9.94 9.9
#> AAGGCATGCG AAGTTCCTTG AATACCGGTA AATCCATCTG AATCGTCCGC
#> NAMPT 14.1 14.24 12.7 14.39 14.2
#> ENSG00000278869 10.4 9.99 10.3 9.87 10.3
#> CABP7-DT 10.4 9.99 10.3 9.87 10.3
#> AATGACCTTC AATGAGAGCA AATGTCAGTG AATTAGGCCG AATTGCGATG
#> NAMPT 14.1 13.8 14.2 14.8 14.0
#> ENSG00000278869 10.2 10.4 10.1 10.3 10.3
#> CABP7-DT 10.2 10.4 10.1 10.3 10.3
#> ACAACAGTCG ACAACCATAC ACAACGGAGC ACAAGCGCGA ACACAATCTC
#> NAMPT 14.2 13.7 13.3 13.9 14.2
#> ENSG00000278869 10.3 11.8 10.5 10.2 9.9
#> CABP7-DT 10.3 10.2 10.5 10.2 9.9
#> ACACAGTGAA ACACCGAATT ACACGCAGTA ACACGGTCCT ACACTTGCTG
#> NAMPT 13.8 10.3 13.3 14.4 12.6
#> ENSG00000278869 11.0 10.3 10.2 10.0 10.3
#> CABP7-DT 11.0 10.3 10.2 10.0 10.3
#> ACAGTGCCAA ACATGTGTGC ACCAGGACCA ACCATAACAC ACCGAACCGT
#> NAMPT 12.6 14.46 14.8 13.9 13.7
#> ENSG00000278869 11.0 9.93 10.1 10.2 10.0
#> CABP7-DT 11.0 9.93 10.1 10.2 10.0
#> ACCGAGAGTC ACCGGTACAG ACCGTACTTC ACCTCCGACA ACCTCTCTCC
#> NAMPT 13.6 13.3 13.6 13.8 13.7
#> ENSG00000278869 10.4 10.5 10.4 10.3 10.2
#> CABP7-DT 10.4 10.5 10.4 10.3 10.2
#> ACCTGTCCGA ACGAATGACA ACGCTGGATA ACGTAGGCAC ACGTGCTGAT
#> NAMPT 13.9 13.38 14.1 13.6 14.1
#> ENSG00000278869 10.4 9.92 10.4 10.4 10.4
#> CABP7-DT 10.4 9.92 10.4 10.4 10.4
#> ACTCCAAGCC ACTGGCGCAT ACTGGCTTCC ACTTAACTGC ACTTCATCAC
#> NAMPT 14.3 14.2 13.2 14.52 13.9
#> ENSG00000278869 10.1 10.1 10.9 9.77 10.2
#> CABP7-DT 10.1 10.1 10.9 9.77 10.2
#> ACTTCGTTGA ACTTCTCCTG ACTTGAGGAA ACTTGTAAGG AGAACCACGG
#> NAMPT 14.0 12.9 13.44 12.8 14.2
#> ENSG00000278869 10.1 10.6 9.98 10.4 10.5
#> CABP7-DT 10.1 10.6 9.98 10.4 10.5
#> AGAAGCAATC AGACCGTTAT AGACTAGCAT AGAGATGCAG AGAGCTTACA
#> NAMPT 14.2 14.21 13.9 14.0 14.3
#> ENSG00000278869 10.1 9.96 10.8 10.3 10.0
#> CABP7-DT 10.1 9.96 10.8 10.3 10.0
#> AGAGTGTAAC AGAGTTCTGC AGATAGTGCT AGCAATGCGC AGCATGTCAT
#> NAMPT 13.7 14.5 13.41 14.0 14.2
#> ENSG00000278869 10.2 10.6 9.95 10.0 10.3
#> CABP7-DT 10.2 10.6 9.95 10.0 10.3
#> AGCCACTAGC AGCCAGAATA AGCCAGCTCT AGCGATAACG AGCTATTCCA
#> NAMPT 14.4 14.05 13.90 13.1 14.36
#> ENSG00000278869 10.1 9.96 9.99 10.3 9.96
#> CABP7-DT 10.1 9.96 9.99 10.3 9.96
#> AGGCGTCTGT AGGTCACCAA AGTAACTCAC AGTAAGCGTT AGTCCACGTA
#> NAMPT 14.6 13.7 13.9 14.1 14.1
#> ENSG00000278869 10.2 10.2 10.2 10.4 12.3
#> CABP7-DT 10.2 10.2 10.2 10.4 10.0
#> AGTCTCGGCA AGTCTGTACG AGTGCAATGT ATAACGCCTC ATAAGAGGTC
#> NAMPT 14.5 13.4 13.8 14.11 14.2
#> ENSG00000278869 10.4 10.2 10.4 9.87 10.5
#> CABP7-DT 10.4 10.2 10.4 9.87 10.5
#> ATAAGGTGCA ATACACGACA ATACCTCCGG ATAGCAGTGC ATAGGCCATT
#> NAMPT 13.6 14.2 13.38 12.6 13.9
#> ENSG00000278869 10.1 10.2 9.92 10.3 10.0
#> CABP7-DT 10.1 10.2 9.92 10.3 10.0
#> ATATCCGCAT ATCAGCACTT ATCAGCGAGG ATCCAATACG ATCCGCTGTG
#> NAMPT 13.2 14.3 14.3 13.84 13.5
#> ENSG00000278869 10.4 10.4 10.4 9.93 10.3
#> CABP7-DT 10.4 10.4 10.4 9.93 10.3
#> ATCCGTCCAT ATCGACGGCT ATCGCGATTA ATCGGTAGGC ATCTAAGGAG
#> NAMPT 13.66 14.3 13.7 13.8 14.4
#> ENSG00000278869 9.96 10.4 10.0 10.1 9.9
#> CABP7-DT 9.96 10.4 10.0 10.1 9.9
#> ATGACGGTAA ATGACTCAGT ATGCGGACTG ATGGTCTTAG ATGTGGAAGC
#> NAMPT 14.5 13.84 14.71 13.3 13.9
#> ENSG00000278869 10.2 9.93 9.85 10.5 10.4
#> CABP7-DT 10.2 9.93 9.85 10.5 10.4
#> ATTATCGGAC ATTCGGAACA CAACAATCCA CAAGAAGCAT CAAGATGAGG
#> NAMPT 14.4 12.8 14.1 13.8 13.76
#> ENSG00000278869 10.3 10.5 10.2 10.3 9.85
#> CABP7-DT 10.3 10.5 10.2 10.3 9.85
#> CAAGCCAACG CAAGTGGATC CACAGTTCAT CACGAGTCTG CACGCTCCAA
#> NAMPT 12.8 14.13 14.0 14.6 14.1
#> ENSG00000278869 11.2 9.89 10.3 10.1 10.4
#> CABP7-DT 11.2 9.89 10.3 10.1 10.4
#> CACTGAGCAC CAGATCAATG CAGTGCTCTT CAGTTAAGCA CATAGCTATC
#> NAMPT 14.4 13.8 14.23 13.8 13.9
#> ENSG00000278869 10.1 10.4 9.98 10.4 10.2
#> CABP7-DT 10.1 10.4 9.98 10.4 10.2
#> CATCACCACC CATGTACGCC CATTACACTG CATTCGACGA CCAACTATGG
#> NAMPT 14.8 13.9 14.1 13.90 12.9
#> ENSG00000278869 10.5 10.0 10.4 9.99 10.6
#> CABP7-DT 10.5 10.0 10.4 9.99 10.6
#> CCAAGGAGTT CCAATTGTTC CCACAAGTGC CCAGCTTAGT CCATAACTTG
#> NAMPT 14.45 14.4 14.46 14.1 13.62
#> ENSG00000278869 9.81 10.3 9.94 10.9 9.72
#> CABP7-DT 9.81 10.3 9.94 10.9 9.72
#> CCATAGATCA CCGAACAAGC CCGAAGACCT CCGAATAGTG CCGACTTCTC
#> NAMPT 14.2 13.6 14.3 14.4 14.7
#> ENSG00000278869 9.8 12.1 10.6 10.0 10.3
#> CABP7-DT 9.8 10.5 10.6 10.0 10.3
#> CCGATCCACT CCGATGATAC CCGCGTTATG CCGCTAGCTT CCGGAGTATC
#> NAMPT 13.6 14.0 13.9 14.1 14.8
#> ENSG00000278869 12.0 10.6 10.2 10.2 10.1
#> CABP7-DT 10.4 10.6 10.2 10.2 10.1
#> CCGGCCAATT CCGGTCTCTA CCGTACGATG CCGTCAGAAC CCTAGACACG
#> NAMPT 14.0 14.6 13.4 14.17 13.9
#> ENSG00000278869 10.3 10.1 10.6 9.77 10.2
#> CABP7-DT 10.3 10.1 10.6 9.77 10.2
#> CCTAGTTGAG CCTATTCTGT CCTCAACCGA CCTCCATAAG CCTGATGCCA
#> NAMPT 14.4 14.8 14.6 14.1 13.95
#> ENSG00000278869 10.2 10.6 10.2 10.2 9.86
#> CABP7-DT 10.2 10.6 10.2 10.2 9.86
#> CCTGCAATAC CCTTGTATTC CGAGATCTCT CGAGGAACAA CGATAACCGC
#> NAMPT 13.5 14.0 13.4 14.7 14.2
#> ENSG00000278869 10.3 10.1 10.6 11.7 10.3
#> CABP7-DT 10.3 10.1 10.6 10.1 10.3
#> CGATCCTGTG CGCCAACCAT CGCCAGTGTT CGCGGATTCA CGCTTCTTGG
#> NAMPT 14.07 13.8 14.5 13.7 14.5
#> ENSG00000278869 9.98 11.4 10.1 10.0 10.3
#> CABP7-DT 9.98 11.4 10.1 10.0 10.3
#> CGGAATACAC CGGAGATTGG CGGAGCTCAA CGGATCGGTA CGGATTCTAG
#> NAMPT 14.1 14.5 14.0 14.50 13.1
#> ENSG00000278869 10.4 10.4 10.3 9.86 10.3
#> CABP7-DT 10.4 10.4 10.3 9.86 10.3
#> CGGCAACTTA CGGCTCATCA CGGTCGTATT CGGTGACATC CGTAACGGAT
#> NAMPT 12.8 14.1 14.2 12.9 14.3
#> ENSG00000278869 10.0 10.4 10.1 10.6 10.1
#> CABP7-DT 10.0 10.4 10.1 10.6 10.1
#> CGTAAGATTC CGTACTGTAA CGTAGAAGAC CGTCCTAGGA CGTCGGCAAT
#> NAMPT 13.6 13.6 14.5 13.89 13.5
#> ENSG00000278869 10.2 10.1 10.4 9.98 10.3
#> CABP7-DT 10.2 10.1 10.4 9.98 10.3
#> CGTGAGTTAT CGTGTCAAGC CTAACTTCAG CTAATAGCGT CTACACCAGG
#> NAMPT 14.2 12.9 14.4 13.9 14.20
#> ENSG00000278869 10.1 10.5 10.0 12.0 9.96
#> CABP7-DT 10.1 10.5 10.0 10.4 9.96
#> CTAGCACAAT CTATGAACGG CTCAAGGACC CTCACCTGTC CTCCTATTGT
#> NAMPT 13.97 14.28 14.0 14.4 13.52
#> ENSG00000278869 9.89 9.89 10.3 10.0 9.82
#> CABP7-DT 9.89 9.89 10.3 10.0 9.82
#> CTCGCAACGT CTGGATTGAC CTGTCTGTGT CTTATGTTGC CTTCATATCG
#> NAMPT 13.9 14.3 13.6 14.1 13.9
#> ENSG00000278869 10.0 10.2 10.4 10.2 9.8
#> CABP7-DT 10.0 10.2 10.4 10.2 9.8
#> CTTGCTGACG CTTGGATCTT GAAGAGTTCT GAAGGATTAG GAATCGAGCC
#> NAMPT 13.5 14.1 14.6 13.9 13.2
#> ENSG00000278869 10.7 10.0 10.2 10.2 10.4
#> CABP7-DT 10.7 10.0 10.2 10.2 10.4
#> GAATCTTCTC GAATTACGGC GACCATCTAA GACGACCACA GAGAACGAAG
#> NAMPT 13.2 14.3 14.17 14.2 14.3
#> ENSG00000278869 10.0 10.4 9.92 10.5 11.7
#> CABP7-DT 10.0 10.4 9.92 10.5 10.1
#> GAGACAAGGC GAGACATCTT GAGCGAGTCA GAGTAGACCA GATACGCTTA
#> NAMPT 14.2 13.3 12.8 13.9 12.7
#> ENSG00000278869 11.9 10.1 10.5 10.0 11.1
#> CABP7-DT 10.3 10.1 10.5 10.0 11.1
#> GATAGACTGT GATAGAGGCG GATAGGTCAA GATATCAGGA GATCTCATTC
#> NAMPT 13.0 13.5 14.2 13.8 13.6
#> ENSG00000278869 10.6 10.7 10.1 10.3 10.1
#> CABP7-DT 10.6 10.7 10.1 10.3 10.1
#> GATCTGGTCG GATGAGTGAC GATGGATACA GATGTGACAG GATTGCACGC
#> NAMPT 13.4 14.23 14.7 14.0 10.9
#> ENSG00000278869 10.3 9.98 10.2 10.1 10.9
#> CABP7-DT 10.3 9.98 10.2 10.1 10.9
#> GCACACTATA GCACTGCGTT GCACTTAATC GCAGGAGATG GCAGTACTGG
#> NAMPT 14.1 13.5 13.88 13.9 14.5
#> ENSG00000278869 10.4 10.3 9.97 10.4 10.0
#> CABP7-DT 10.4 10.3 9.97 10.4 10.0
#> GCATATGAGT GCATCCGATC GCCAAGTACA GCCACGATTC GCCATAGGTT
#> NAMPT 14.5 14.3 13.4 14.4 13.7
#> ENSG00000278869 10.2 10.0 10.3 10.0 10.2
#> CABP7-DT 10.2 10.0 10.3 10.0 10.2
#> GCCATATCGA GCCGTCAATA GCCTGGACAT GCGTAATTAC GCTATTATCC
#> NAMPT 14.14 13.8 14.09 13.8 13.49
#> ENSG00000278869 9.89 10.3 11.43 10.4 9.79
#> CABP7-DT 9.89 10.3 9.84 10.4 9.79
#> GCTCAGTAAT GCTGCTTATA GGAATAAGCA GGACGATGCT GGCATCGTGA
#> NAMPT 13.6 13.8 14.3 12.4 13.6
#> ENSG00000278869 10.8 10.1 10.4 10.1 10.4
#> CABP7-DT 10.8 10.1 10.4 10.1 10.4
#> GGCATTATTG GGCCGAGATT GGCGCTATAA GGCGTTAAGT GGCTATTGAT
#> NAMPT 14.0 13.6 14.16 13.7 13.2
#> ENSG00000278869 10.1 10.2 11.50 10.2 10.0
#> CABP7-DT 10.1 10.2 9.91 10.2 10.0
#> GGCTGCTACT GGTAATGTGT GGTGTTCACC GGTTCACTGG GTAACCAGTA
#> NAMPT 13.8 14.3 14.5 14.0 13.6
#> ENSG00000278869 10.3 10.0 10.2 10.6 10.2
#> CABP7-DT 10.3 10.0 10.2 10.6 10.2
#> GTAACCTTGG GTAAGAACCT GTAAGGCTCC GTAATCCACG GTATTGTGGA
#> NAMPT 13.7 13.8 13.7 13.5 14.2
#> ENSG00000278869 10.0 10.1 10.2 10.0 10.1
#> CABP7-DT 10.0 10.1 10.2 10.0 10.1
#> GTCCGCATCA GTCCTTCGGT GTCGCTCTCT GTCGGTGACA GTCTCGAGTG
#> NAMPT 14.1 15.1 14.0 13.31 13.6
#> ENSG00000278869 10.4 10.2 10.3 9.85 10.5
#> CABP7-DT 10.4 10.2 10.3 9.85 10.5
#> GTCTCTTAAG GTCTTCCGAG GTGACTATAC GTGGTTAATG GTGTGCCTGT
#> NAMPT 14.3 13.7 13.94 14.2 13.7
#> ENSG00000278869 10.4 10.5 9.86 10.3 10.3
#> CABP7-DT 10.4 10.5 9.86 10.3 10.3
#> GTGTGTGTCC GTTCATTGCC GTTCCGGTGA GTTCGTCGAA GTTGAATTGG
#> NAMPT 14.3 14.2 13.3 13.87 13.6
#> ENSG00000278869 10.2 10.1 10.5 9.96 10.4
#> CABP7-DT 10.2 10.1 10.5 9.96 10.4
#> GTTGATCCGC GTTGTATGCT TAACCGTAGC TAACGTCGAT TAAGGTACGG
#> NAMPT 12.70 14.04 14.3 14.1 14.60
#> ENSG00000278869 9.89 9.96 10.1 10.2 9.84
#> CABP7-DT 9.89 9.96 10.1 10.2 9.84
#> TACTACCGCC TAGCGCCAAC TAGGTTGCAA TAGTAGTCTC TAGTCCGCTG
#> NAMPT 14.57 13.5 14.0 14.28 13.6
#> ENSG00000278869 9.93 10.7 10.3 9.89 10.5
#> CABP7-DT 9.93 10.7 10.3 9.89 10.5
#> TAGTGGAACT TATCATGCAG TATCGTTACG TCAAGTGCAG TCACAGATAC
#> NAMPT 12.6 13.3 14.0 13.8 14.6
#> ENSG00000278869 10.3 10.2 10.1 10.3 10.0
#> CABP7-DT 10.3 10.2 10.1 10.3 10.0
#> TCACCGCCTA TCACGCCACT TCACGTTGGC TCATTGTCCA TCCACACTAG
#> NAMPT 14.0 14.0 13.5 14.6 13.0
#> ENSG00000278869 10.3 10.1 10.3 10.1 10.2
#> CABP7-DT 10.3 10.1 10.3 10.1 10.2
#> TCCACGGTCA TCCACTCGCT TCCGACTAAC TCCGTTATCT TCCTAAGAGA
#> NAMPT 14.6 12.3 14.7 14.1 14.3
#> ENSG00000278869 10.1 10.8 10.2 10.2 10.4
#> CABP7-DT 10.1 10.8 10.2 10.2 10.4
#> TCCTCTAGTA TCGAAGCATT TCGAGAGAGC TCGCACTTGA TCGCCTACTG
#> NAMPT 13.6 13.8 12.0 14.83 12.7
#> ENSG00000278869 10.8 10.6 10.4 9.88 10.4
#> CABP7-DT 10.8 10.6 10.4 9.88 10.4
#> TCGCGTAGCA TCGGCGTTAA TCTACATCCG TCTCTCCTAT TGAAGAAGGT
#> NAMPT 13.5 14.4 14.6 14.93 14.9
#> ENSG00000278869 10.4 10.0 10.5 9.97 10.3
#> CABP7-DT 10.4 10.0 10.5 9.97 10.3
#> TGAGCGTTCC TGAGTACGTA TGGAATGGAG TGTCATTCGC TGTGCTTCAG
#> NAMPT 14.5 13.3 13.7 14.6 14.20
#> ENSG00000278869 10.1 10.5 10.2 10.5 11.53
#> CABP7-DT 10.1 10.5 10.2 10.5 9.95
#> TGTTCAGGAT TTACACACGT TTACTGTGAC TTATGCCGCG TTCACGGAAG
#> NAMPT 13.6 14.57 14.5 14.5 14.3
#> ENSG00000278869 10.2 9.71 10.6 10.1 10.4
#> CABP7-DT 10.2 9.71 10.6 10.1 10.4
#> TTCGAGTGAT TTCTGTACCT TTGGTAACAG
#> NAMPT 14.6 14.2 14.30
#> ENSG00000278869 10.2 10.7 9.91
#> CABP7-DT 10.2 10.7 9.91
#> [ reached getOption("max.print") -- omitted 497 rows ]