For the moment, I will assume we only want to deal with the 8 samples. However, I will try a count-filtered run, an annotation filtered run, and both.
keepers <- list(
"embryo" = c("embryogenic", "nonembryogenic"))
k8_count_de <- sm(all_pairwise(k8_count))
k10_count_de <- sm(all_pairwise(k10_count))k8_count_tables <- sm(combine_de_tables(
k8_count_de, keepers=keepers, type="deseq",
excel=paste0("excel/k8_count_by_gene_de-v", ver, ".xlsx"),
abundant_excel=paste0("excel/k8_count_by_gene_abundant-v", ver, ".xlsx"),
sig_excel=paste0("excel/k8_count_by_gene_sig-v", ver, ".xlsx")))
k10_count_tables <- sm(combine_de_tables(
k10_count_de, keepers=keepers, type="deseq",
excel=paste0("excel/k10_count_by_gene_de-v", ver, ".xlsx"),
abundant_excel=paste0("excel/k10_count_by_gene_abundant-v", ver, ".xlsx"),
sig_excel=paste0("excel/k10_count_by_gene_sig-v", ver, ".xlsx")))k8k10_comparison <- compare_de_results(k8_count_tables, k10_count_tables)
extract_fasta_sequences <- function(k8_count_tables) {
sig_table <- k8_count_tables[["significant"]][["deseq"]][["ups"]][[1]]
subset_df <- sig_table[, c("transcriptid", "transcriptseq")]
names <- subset_df[[1]]
sequences <- subset_df[[2]]
seq <- as.list(sequences)
names(seq) <- names
testing <- seqinr::write.fasta(seq, names, file.out="test_ups.fasta")
sig_table <- k8_count_tables[["significant"]][["deseq"]][["downs"]][[1]]
subset_df <- sig_table[, c("transcriptid", "transcriptseq")]
names <- subset_df[[1]]
sequences <- subset_df[[2]]
seq <- as.list(sequences)
names(seq) <- names
testing <- seqinr::write.fasta(seq, names, file.out="test_downs.fasta")
}In the sample estimation worksheet, we created a list of genes putatively strongest in terms of the signal from the principal component associated with batch (Comp 2). Let us look at the differential expression data and see where these genes lie.
test_batch_idx <- rownames(k8_count_tables[["data"]][[1]]) %in% most_by_batch
test_batch <- k8_count_tables[["data"]][[1]][test_batch_idx, ]
strong_batch_de_idx <- abs(test_batch[["deseq_logfc"]] > 1) & test_batch[["deseq_adjp"]] <= 0.05
strong_batch_de <- test_batch[strong_batch_de_idx, ]
## The following genes are not to be trusted I think.
knitr::kable(strong_batch_de)| geneid | transcriptid | blastxname | blastxqueryloc | blastxhitloc | blastxidentity | blastxevalue | blastxrecname | blastxtaxonomy | blastpname | blastpqueryloc | blastphitloc | blastpidentity | blastpevalue | blastprecname | blastptaxonomy | rrnasubunit | rrnasubunitregion | protid | protcoords | pfamdata | signalpdata | tmhmmexpaa | tmhmmhelices | tmhmmtopology | eggnogid | eggnogdescription | keggdata | geneontologyblast | geneontologypfam | transcriptseq | peptide | length | limma_logfc | limma_adjp | deseq_logfc | deseq_adjp | edger_logfc | edger_adjp | limma_ave | limma_t | limma_b | limma_p | deseq_basemean | deseq_lfcse | deseq_stat | deseq_p | edger_logcpm | edger_lr | edger_p | basic_nummed | basic_denmed | basic_numvar | basic_denvar | basic_logfc | basic_t | basic_p | basic_adjp | limma_adjp_fdr | deseq_adjp_fdr | edger_adjp_fdr | basic_adjp_fdr | lfc_meta | lfc_var | lfc_varbymed | p_meta | p_var | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TRINITY_DN10128_c0_g1 | TRINITY_DN10128_c0_g1 | TRINITY_DN10128_c0_g1_i1 | 0.00 | 1 | 0.00 | 1 | 0.00 | 0 | TTGAGATATAGTTGATTGATTGATTGGAACAGTTGAATTGCGAGTAAACTGATTACCGATATAGATAGATTTATTGAGATAGAGTTGATTGATCGATTGAAACAATTGAATTGCGAGTAACTGAGTGTAGATATAGATAGATTGGTTGAGATTGAGATATAGTTGATTGATTGAAAGTTGAAACAGTTGAATTGTGAGTAAACTGAATACAAATATAGATAGATTGGTTGAGATTGATATATAGTTGATTGATTGAAACAGTTGAATTGTGAGTAAACTGAATACAAATATAGATAGATTGGTTGAGATTGAGATATAGTTGATTGATTGAAACAGCTGAATTGTGAGTAAACTGAATACAGATATAGATAGATTTATTGAGATTGAGATACAGTTGATTGATTGATTGAAACAGTTGAATTGTGAGTAAACTGAATACAAATATAGATAGATTGGTTGAGATTGATATATAGTTGATTGATTGAAACAGTTGAATTGTGAGTAAACCGAATACAAATATAGATAGATTTATTGAGATTGAGATATAGATGATTGATTGATTGAAACAGTTGAATTGCGAGTAAACAAAATATCGATATAGATAGATTTATTGAGATTGAGATACAGTTGATTGATTGATTGAAACAGTTGACTTGTGAGTAAACTGAATA | 671 | 2.144 | 0.1032 | 2.645 | 0.0323 | 2.456 | 0.0544 | 0.2185 | -3.142 | -2.332 | 0.0074 | 24.52 | 0.9289 | 2.848 | 0.0044 | 1.608 | 8.642 | 0.0033 | 0.5070 | 1.779 | 3.561e+00 | 1.093e+00 | 1.272 | 1.413 | 2.207e-01 | 5.090e-01 | 1.032e-01 | 6.695e-03 | 5.008e-03 | 2.847e-01 | 2.557 | 1.502e+00 | 5.874e-01 | 5.035e-03 | 4.570e-06 | |||||||||||||||||||||||
| TRINITY_DN11001_c0_g7 | TRINITY_DN11001_c0_g7 | TRINITY_DN11001_c0_g7_i1 | 0.00 | 1 | 0.00 | 1 | TRINITY_DN11001_c0_g7::TRINITY_DN11001_c0_g7_i1::g.168124::m.168124 | 86-1168[+] | 0.00 | 0 | GGTATCAACGCAGAGTACGGGGCTCACTCAAAAATCTCCGCCCTAATACCAAATCCCAATTCTTCAAGCTCTCTTTCTCTTATCAATGGCGACAATGGCTTCCACCTTGGCTTCCTCCGTGATTTCCAAGACAAAGTTCCTTGACACACACAAATCATCATCCTTGTATGGTGTGCCAATTTCCTCACAAGCTAGATTGAAAATCGTAAAATCGACTCACCAGAACATGTCTGTTTCTATGTCTGCTGATGCTTCTCCTCCTCCGCCTTACGATCTCGGAAGTTTCAGTTTTAATCCGATTAAGGAATCGATTGTTGCTCGGGAAATGACACGTAGGTACATGACGGATATGATCACTTATGCTGATACTGACGTCGTCGTTGTTGGTGCTGGATCTGCTGGTCTATCTTGTGCTTATGAGCTCAGCAAGAACCCTGATGTTCAGGTGGCCATCCTTGAGCAATCTGTGAGCCCTGGTGGAGGTGCTTGGCTAGGCGGACAACTCTTCTCAGCTATGATTGTGCGTAAGCCAGCACATCTTTTCTTGAACGAGCTAGGCATTGACTACGACGAGCAAGACAACTACGTGGTCGTCAAGCACGCTGCCTTGTTTACCTCGACCATCATGAGCAAGCTTTTGGCCAGGCCAAATGTGAAGCTCTTCAATGCTGTTGCAACAGAGGACCTTATCGTGAAGAACGGAAGAGTTGGTGGTGTTGTCACCAACTGGTCTTTGGTTTCCCAGAACCATGACACACAATCCTGCATGGACCCTAATGTTATGGAGGCTAAGGTTGTGGTTAGCTCCTGCGGCCACGACGGTCCCATGGGTGCCACTGGTGTTAAGAGGCTTAGGAGCATTGGCATGATTAACAGTGTTCCTGGAATGAAAGCTTTGGATATGAACACTGCTGAGGATGCAATTGTTAGACTTACCAGAGAAGTTGTACCTGGAATGATTATAACAGGGATGGAAGTTGCTGAAATTGATGGAGCACCAAGAATGGGTCCAACTTTTGGAGCTATGATGATATCAGGGCAGAAGGCTGCGCACCTTGCCCTACGGGCGTTGGGATTGCCCAACGCCCTTGACGGAACTGCAGAAACAAGCATCCACCCGGAGCTTATGTTGGCTGCAGCTGATGAAGCTGAAACTGCTGATGCTTAAATGTAATTATAGTTCCTAAGAAAGGATATGAGAAATATTAGTTTTTCCTAGATGAGCATGGTTGTGTGATGGAGATAAATTGGCTAGTTGGGGATGAATAAAAATCTGCGAGACCTTTGTCTGTTTCATGTCAATTCTTCTTTTACTTTTGATTTATTTTGGGACTTAGAAACTATATGTGAAAAAAGTGGTAAGAGTAAGACTTGTTTTAGTCGTTGAATAATCCTATGGGCCTCATTTTGGTACTTGATGTGGTTTGGGCCTCGCGGGAGAAGCTGTCTCTTATAC | 1456 | 2.442 | 0.0992 | 2.884 | 0.0098 | 2.763 | 0.0468 | 0.8301 | -3.175 | -2.321 | 0.0069 | 47.12 | 0.8753 | 3.295 | 0.0010 | 2.490 | 9.033 | 0.0027 | 0.4770 | 2.438 | 5.537e+00 | 1.171e+00 | 1.961 | 1.636 | 1.735e-01 | 4.583e-01 | 9.918e-02 | 1.533e-03 | 4.059e-03 | 2.303e-01 | 2.800 | 1.451e+00 | 5.180e-01 | 3.529e-03 | 9.466e-06 | |||||||||||||||||||||
| TRINITY_DN17811_c0_g5 | TRINITY_DN17811_c0_g5 | TRINITY_DN17811_c0_g5_i1 | AZF2_ARATH | 866-375 | 67-187 | 32.12 | 0 | Zinc finger protein AZF2; | Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | AZF2_ARATH | 128-353 | 67-242 | 30.87 | 0 | Zinc finger protein AZF2; | Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | TRINITY_DN17811_c0_g5::TRINITY_DN17811_c0_g5_i1::g.74924::m.74924 | 177-1247[-] | 22.83 | 1 | i12-34o | COG5048 | Zinc finger protein | KEGG:ath:AT3G19580 | GO:0005634,cellular_component,nucleus; GO:0003677,molecular_function,DNA binding; GO:0046872,molecular_function,metal ion binding; GO:0043565,molecular_function,sequence-specific DNA binding; GO:0003700,molecular_function,transcription factor activity, sequence-specific DNA binding; GO:0044212,molecular_function,transcription regulatory region DNA binding; GO:0009738,biological_process,abscisic acid-activated signaling pathway; GO:0009793,biological_process,embryo development ending in seed dormancy; GO:0042538,biological_process,hyperosmotic salinity response; GO:0045892,biological_process,negative regulation of transcription, DNA-templated; GO:0009737,biological_process,response to abscisic acid; GO:0010200,biological_process,response to chitin; GO:0009414,biological_process,response to water deprivation; GO:0006351,biological_process,transcription, DNA-templated | AAAGTAAACTACCAACAATACTTGATGAAAACAACAACAAAAAAAAAAAAAATTAATTTAGGAAACAAATTTATGTATATTTATGAACAACAATAATTCTAAAAATTCATTATCACAAATTTTTGTGACTAATTAATTGATCAATAAGTGTAAAAAAAAATGAAAAACTAAAATTATTAGTAATAGCAATCAACCAAAGGGGCTGCAGATAACACAAGACTTTGTTCAAATTTGTGATCATCTTCTGATGGTGCTGGTAAATTAAGATCAAGAGATAATATATTTCTTCTTGATTTTTCGTCGTGATGGGATGAAGATGATTCTGAAACATTATTGTTTGTAGTAGAGGTTGTCATCGCTGTAGGAGGTGGTCTGTGTCTTCTCATGTGTCCACCTAAAGCTTGTCCCGATGAAAACTCCGATCCACAAATTGAACATTCGTGGATTTTGGTCTTGATGTTATTAACAACTATTTTGTTTGAGAGAGATGTACTATTAATTTTATTGAGACGCCCTTGATCCTTATCGTTCTCTAGATGATGATGATGTGAATCATCATGACCGCCACCACTAGCAGTGCCAGTATTGATAGTGACAGATTTTTTCTCTTCCACTATGGTTTTGGGCTTTTTGTGACTTGCTCTGTGTCCACCAAGTGCTTGAAATGAAGGGAAAGTTCTATTGCAAGTTTTGCATTCATAGACATAAAAGCCAGCTTTTCCAGTTGTACTATTACTAGTGGTCATTTCTGCAAATTTCCTACTGCTGATTTTCTCCTTTTTGACTTCACTTATTACATCTTGTACTTTCTGGCCACATCCACTTTGTGCTAATAGAATTAAACAATTAGCCATATCTTCATCTTCCTCAGATGTGCTAGTTGTTGAAATTTGAGTAGTAGAAATGGTTGGTGAATATTGAATATTTGTTGACTTGTAAAAATCACCTCCGCTACCACCATCACCACCACCAGCATCATCGCTTCCACCAGCGATCGATGAGCTGGTGGTAGTGACAGTCGTCGTCCCCGCTATATTAAGTGGGGACGATGGTCGCGATCGCTTAGTGCGCTTTCCTTTGAAAGCGCATGAGCGATCGGTGAAGTTTTGACTCAAAACTTCCATGACTGCAGAAACAAGAAAAGAAGGCAAAACAAGTGACAAAGTGAACAAGAAGAAGAGTGATAGAAAGAAAGAATATAAAGAGAGAGAAAGAGTGATGTAATTATCCCGTACTCTGCGTTGATAC | 1248 | 2.803 | 0.0092 | 2.995 | 0.0006 | 2.901 | 0.0006 | 0.4279 | -5.071 | 1.004 | 0.0002 | 41.17 | 0.7266 | 4.122 | 0.0000 | 2.352 | 19.200 | 0.0000 | 0.3112 | 2.383 | 3.526e+00 | 4.157e+00 | 2.072 | 1.445 | 1.989e-01 | 4.854e-01 | 9.166e-03 | 5.997e-05 | 1.895e-05 | 2.597e-01 | 3.006 | 1.448e+00 | 4.815e-01 | 7.826e-05 | 8.776e-09 | ||||||
| TRINITY_DN8597_c0_g1 | TRINITY_DN8597_c0_g1 | TRINITY_DN8597_c0_g1_i1 | ISP4_SCHPO | 22-939 | 455-755 | 40.07 | 0 | Sexual differentiation process protein isp4; | Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces | ISP4_SCHPO | 8-313 | 455-755 | 40.07 | 0 | Sexual differentiation process protein isp4; | Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces | TRINITY_DN8597_c0_g1::TRINITY_DN8597_c0_g1_i1::g.50377::m.50377 | 1-1014[+] | 163.33 | 8 | o15-36i43-65o75-97i129-151o201-223i228-245o250-267i279-301o | KEGG:spo:SPBC29B5.02c | GO:0005783,cellular_component,endoplasmic reticulum; GO:0005789,cellular_component,endoplasmic reticulum membrane; GO:0005794,cellular_component,Golgi apparatus; GO:0016021,cellular_component,integral component of membrane; GO:0005886,cellular_component,plasma membrane; GO:1901584,molecular_function,tetrapeptide transmembrane transporter activity; GO:0015031,biological_process,protein transport; GO:1901583,biological_process,tetrapeptide transmembrane transport | GTATCAACGCAGAGTACGGGGATGAAGAGTTACAAGCAAGTCCCTCAGTGGTGGTTCCTCGCATTATTGGTAGGTAGCATAGCCCTATCACTTGTGATGTGTTTTGTGTGGAAAGAAGACGTGCAGCTGCCGTGGTGGGGCATGTTGTTTGCGTTTGGTCTTGCTTTTATTGTTACTCTCCCTATAGGGGTCATTCAAGCGACTACCAATCAGCAACCTGGATATGACATAATTGCACAGTTCATAATTGGTTATATCCTCCCAGGGAAACCAATCGCGAACTTGCTTTTCAAAATATATGGCCGGACAAGTACTGTTCATGCTCTCTCCTTTTTAGCCGATCTTAAACTTGGTCACTACATGAAAATTCCGCCACGATGCATGTACACAGCTCAGCTCGTGGGGACACTGGTTGCTGGTACAATCAACCTTGCTGTAGCATGGTGGATGTTAGGAAGCATCGAGAACATTTGTGACGTTGAGACTCTTCATCCGGACAGCCCATGGACCTGTCCTAAATTCCGAGTGACTTTTGATGCATCTGTCATATGGGGTCTGATTGGACCACAACGGTTATTTGGTCCCGGAGGATTATACAGGAACTTGGTATGGTTATTCCTTATAGGTGCATTGCTACCGGTGCCTATTTGGGTGTTAAGCAAAATCTTCCCGGAAAAGAAATGGATCCCATTGATCAACATACCTGTTATATCATATGGTTTCGCGGGAATGCCACCAGCCACACCAACGAATATTGCTAGCTGGCTTATAACGGGTATGATATTCAACTATTTCGTGTTCAAATACAGAAAAGAATGGTGGAAGAAATACAACTATGTTCTGTCAGCCGCGTTGGATGCTGGAACAGCTTTTATGGGTGTTTTATTGTTTTTCGCGTTGCAAAACGAGGGTAAAAACTTGAAATGGTGGGGAACAGAGTTAGACCATTGTCCCTTAGCAACTTGTCCAACAGCCCCTGGGATCATAGTGGAAGGATGTCCAGTTTTCAAGTAGGCCTAACAACAAGAATGAATGGTTCTAAGCATTGTTGATGTAATTTTGATAGTTTTTTTGTGTTGTTCAACTAAATATATTTTGTTATGAGAGTTTTCTGATCTTGTTTGCAGATGAGCTAATGAAAGACAAAATATTGTGAATTGAAATTGTGATTAACTTTTTACTAAATCAAAATATTGTTAAT | 1201 | 2.184 | 0.2483 | 2.724 | 0.0492 | 2.533 | 0.1689 | 0.4656 | -2.341 | -3.715 | 0.0350 | 35.02 | 1.0200 | 2.669 | 0.0076 | 2.218 | 5.484 | 0.0192 | 0.0566 | 2.195 | 6.038e+00 | 1.931e+00 | 2.139 | 1.111 | 3.196e-01 | 5.966e-01 | 2.482e-01 | 1.145e-02 | 2.761e-02 | 3.918e-01 | 2.607 | 1.515e+00 | 5.813e-01 | 2.060e-02 | 1.891e-04 | ||||||||
| TRINITY_DN9223_c1_g4 | TRINITY_DN9223_c1_g4 | TRINITY_DN9223_c1_g4_i1 | EB1C_ARATH | 118-1104 | 1-323 | 62.46 | 0 | Microtubule-associated protein RP/EB family member 1C; | Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | EB1C_ARATH | 40-368 | 1-323 | 62.46 | 0 | Microtubule-associated protein RP/EB family member 1C; | Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | TRINITY_DN9223_c1_g4::TRINITY_DN9223_c1_g4_i1::g.67832::m.67832 | 1-1119[+] | 0.00 | 0 | COG5217 | microtubule-associated protein RP EB family member | KEGG:ath:AT5G67270; KO:K10436 | GO:0005618,cellular_component,cell wall; GO:0005874,cellular_component,microtubule; GO:0005730,cellular_component,nucleolus; GO:0005634,cellular_component,nucleus; GO:0009524,cellular_component,phragmoplast; GO:0005819,cellular_component,spindle; GO:0008017,molecular_function,microtubule binding; GO:0051301,biological_process,cell division; GO:0030865,biological_process,cortical cytoskeleton organization; GO:0007067,biological_process,mitotic nuclear division; GO:0009652,biological_process,thigmotropism | GGTATCAACGCAGAGTACGGGGAAACCCTCATTTCAAACTCTCTTTCTCTCTCCGTCCGCCCTCTCTCTCTCTCTCTTTCTACAGAGCCTTCTAGAGATCTTCTCCGAAGAGGAGAAATGGCAGCACACATAGGAATGATGGATGGGGCATACTTCGTTGGCAGATCGGAAATCCTGGCTTGGATCAATTCCACACTTCATCTTAATCTTTCCAAAGTCGAAGAGGCGTGTACTGGCGCGGTTCATTGCCAGCTAATGGATGCGGCTCACCCAGGGCTAGTCCCTATGCACAAGGTCAATTTTGATGCGAAGAATGAATATGAGATGATCCAGAACTATAAGGTTCTTCAGGATGTATTCACCAAACTCAAGATAACCAAGCACATTGAGGTCAGCAAACTGGTGAAAGGAAGACCTCTTGACAACCTGGAGTTCATGCAATGGATGAAGAGATACTGCGATTCTGTTAATGGAGGCAATATTCACAGTTACAATCCTCTTGAAAGAAGGGAAGGCTGCAAGGGTGCCAAAGAACTGAACAAAAGATCTGCCCCTTCACAAAATGCTACCAAAAATGCCTCAACTGCTTCAAAGCATGTCACCCATAACACTAGAAGAATTGATGTACCTCATGTAAGCAGCACAAGTCAATCTGGTAAGATCTCCAGGCCTTCTTCAAGTGGAGGAGCGTCAACCTATTCTGAAACAGAACGTACAGCACATGAACAACAGATTACGGAGTTGAAGTTATCAGTGGATAGTCTTGAAAAGGAAAGGGACTTCTACTTTTCAAAGTTGAGGGACATTGAAATCCTGTGCCAATGTCCAGAGATTGAAAACCTACCTGTGGTTGAAGCAGTGAAGAGGATTCTGTATGCTATGGATGATGATGCATCACTGGTAGATACTGAAGCCATGATATCTGAGCAACACCAGCAAGTAGAGACATTGAGTTGCATATCTGAAGAGGCAGAAGAAAGGCTGAGGGTAGACACTCAAAAGAGAAAAAACATTGTCAATGTTGACGTTGACCATGCTGCCAGCAACACATTGTCTCCAAGGCAAAGGATGGCTGATGCTTCTGATGTCCATTGCAGTGGATCACTTGTGACATATTGATCAACCTTGTCTCCTGGATAAGTAACTTGTTCTATCTGGGTTGTGGAATAATTCCTGCTACCGTCTTTGTTACTCTGTAGTTAGTTATATGTTGTCAGAGCATACTTTATTTCTAAGCAATACCGTTTGAGGAATTCCATCAGTATAGAAGTAGTGAATATATGAACCTATCTGGTTTGTCTGATTGTCGGTGTACAACATTGCCCGATGTTATTGCTGTTGTATACTGCATTGTAGTGCAAGTCTTGGATTATGATGATTCCTGTGGTTTAATGGATACTAAAGTTGGTATTGGTATTGGTTTTGATTTTAGAAAATATCTTGAAAACAAACATAAGGTAAATTGACAGTCTCCACACAACTTAGT | 1486 | 1.297 | 0.4481 | 2.497 | 0.0432 | 2.374 | 0.2114 | 1.0040 | -1.681 | -4.864 | 0.1156 | 47.83 | 0.9164 | 2.725 | 0.0064 | 2.462 | 4.792 | 0.0286 | 1.2260 | 2.853 | 6.885e+00 | 6.604e-01 | 1.626 | 1.249 | 2.873e-01 | 5.698e-01 | 4.480e-01 | 9.701e-03 | 4.024e-02 | 3.577e-01 | 2.162 | 1.865e+00 | 8.627e-01 | 5.020e-02 | 3.330e-03 | |||||||
| TRINITY_DN9367_c2_g7 | TRINITY_DN9367_c2_g7 | TRINITY_DN9367_c2_g7_i1 | 0.00 | 1 | 0.00 | 1 | TRINITY_DN9367_c2_g7::TRINITY_DN9367_c2_g7_i1::g.195987::m.195987 | 1-459[+] | 30.82 | 1 | i21-38o | GGTATCAACGCAGAGTACGGGACAAACAAATTCATCATACAAAACAATATGGCTTCTAATACTTTTTCTATTCTCATTCTTGTTGTGTCTTTATTTTTGTCTCAGTTCTCATTTTCTTTTGGTGATGGTCCCATACCAGTTGTTCACCTCATTAGCAACTTGACTCCTGGTCATACACCAACTATGCAAGTTACTTGTAAATTACAACATTGGCTCCCTTTGCTTAGTGTAACTTTAGTAATAGGCCAAGATTTTCCATTTGATGCTGGTATTATCAATGATATATATGTATGTTATGCTGAATGGGGTGTATTTTATGCTTGGTTTAATGCATATGATCCACTTAAGGAAGACAAAGGCCAACCTGTTGTCTATTTTTCTTTTCGAGATCGCGGTGTTTATAAGAGTTACGATAAAGCTACTTGGACTGGAGTTACAGATTGGAACAACGGACACTAGCTTTTCGTATTTTTATCATGTCAAGATCGAATTTCGAATTTTTTCTTTATGATAAAAATAAAATTATATAATTTGTGTGTGTGAGTCAAGGTGACGGATGATCTGAATGGGCTTCTTAATTCCCCCGGCAATTGTTTGTTTTTGTCTAGGGTTTTCTTGTTATTTTATTGTCTCTTTGATTCACATTAGTATATTGGTTTTATACTACTTTTTTTTTTCATCTACATTTTTGTTATTGTTCTAATTTATGTGGTTAAAAGGCAACCAAATTGAAAAACTTATATAAAATGCATCAACTTTATTTATACGGTAAAAGTTATCATTAACTAGTATTTATAT | 798 | 2.340 | 0.1089 | 2.939 | 0.0089 | 2.811 | 0.0436 | 0.7559 | -3.092 | -2.448 | 0.0082 | 37.64 | 0.8836 | 3.326 | 0.0009 | 2.170 | 9.212 | 0.0024 | 0.5538 | 2.600 | 4.703e+00 | 3.898e-01 | 2.047 | 1.870 | 1.451e-01 | 4.256e-01 | 1.089e-01 | 1.370e-03 | 3.687e-03 | 1.965e-01 | 2.786 | 1.499e+00 | 5.382e-01 | 3.822e-03 | 1.483e-05 |
k8_conf_de <- sm(all_pairwise(k8_conf, parallel=FALSE))k8_conf_tables <- sm(combine_de_tables(
k8_conf_de, keepers=keepers,
excel=paste0("excel/k8_conf_de-v", ver, ".xlsx"),
sig_excel=paste0("excel/k8_conf_sig-v", ver, ".xlsx")))k8_conf_count_de <- sm(all_pairwise(k8_conf_count, parallel=FALSE))k8_conf_count_tables <- sm(combine_de_tables(
k8_conf_count_de, keepers=keepers,
excel=paste0("excel/k8_conf_count_de-v", ver, ".xlsx"),
sig_excel=paste0("excel/k8_conf_count_sig-v", ver, ".xlsx")))if (!isTRUE(get0("skip_load"))) {
pander::pander(sessionInfo())
message(paste0("This is hpgltools commit: ", get_git_commit()))
this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to ", this_save))
tmp <- sm(saveme(filename=this_save))
}