Table cross used to cross search and merge results in two tables.
Source:R/table_cross.R
table_cross.RdTable cross used to cross search and merge results in two tables.
Arguments
- data1
Dataframe: Shared DEGs of all paired comparisons in all samples expression dataframe of RNA-Seq. (1st-col: Genes, 2nd-col~: Samples).
- data2
Dataframe: GO and KEGG annotation of background genes (1st-col: Genes, 2nd-col: biological_process, 3rd-col: cellular_component, 4th-col: molecular_function, 5th-col: kegg_pathway).
- inter_var
Character: Intersecting variable (column name). Default: "geneID" in example data.
- left_index
Logical: left table as index. Default: TRUE, options: TRUE, FALSE.
- right_index
Logical: right table as index. Default: FALSE, options: TRUE, FALSE.
Examples
# 1. Library TOmicsVis package
library(TOmicsVis)
# 2. Use example dataset
data(gene_expression2)
head(gene_expression2)
#> Genes CT_1 CT_2 CT_3 LT20_1 LT20_2 LT20_3 LT15_1 LT15_2 LT15_3 LT12_1
#> 1 ACAA2 24.50 39.83 55.38 114.11 159.32 96.88 169.56 464.84 182.66 116.08
#> 2 ACAN 14.97 18.71 10.30 71.23 142.67 213.54 253.15 320.80 104.15 174.02
#> 3 ADH1 1.54 1.56 2.04 14.95 13.60 15.87 12.80 17.74 6.06 10.97
#> 4 AHSG 0.00 1911.99 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> 5 ALDH2 2.07 2.86 2.54 0.85 0.49 0.47 0.42 0.13 0.26 0.00
#> 6 AP1S3 6.62 14.59 9.30 24.90 33.94 23.19 24.00 36.08 27.40 24.06
#> LT12_2 LT12_3 LT12_6_1 LT12_6_2 LT12_6_3
#> 1 497.29 464.48 471.43 693.62 229.77
#> 2 305.81 469.48 1291.90 991.90 966.77
#> 3 10.71 30.95 9.84 10.91 7.28
#> 4 0.00 0.00 0.00 0.00 0.00
#> 5 0.28 0.11 0.37 0.15 0.11
#> 6 38.74 34.54 62.72 41.36 28.75
data(gene_go_kegg)
head(gene_go_kegg)
#> Genes
#> 1 FN1
#> 2 14-3-3ZETA
#> 3 A1I3
#> 4 A2M
#> 5 AARS
#> 6 ABAT
#> biological_process
#> 1 GO:0003181(atrioventricular valve morphogenesis);GO:0003128(heart field specification);GO:0001756(somitogenesis)
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 GO:0006419(alanyl-tRNA aminoacylation)
#> 6 GO:0009448(gamma-aminobutyric acid metabolic process)
#> cellular_component
#> 1 GO:0005576(extracellular region)
#> 2 <NA>
#> 3 GO:0005615(extracellular space)
#> 4 GO:0005615(extracellular space)
#> 5 GO:0005737(cytoplasm)
#> 6 <NA>
#> molecular_function
#> 1 <NA>
#> 2 GO:0019904(protein domain specific binding)
#> 3 GO:0004866(endopeptidase inhibitor activity)
#> 4 GO:0004866(endopeptidase inhibitor activity)
#> 5 GO:0004813(alanine-tRNA ligase activity);GO:0005524(ATP binding);GO:0000049(tRNA binding);GO:0008270(zinc ion binding)
#> 6 GO:0003867(4-aminobutyrate transaminase activity);GO:0030170(pyridoxal phosphate binding)
#> kegg_pathway
#> 1 ko04810(Regulation of actin cytoskeleton);ko04510(Focal adhesion);ko04151(PI3K-Akt signaling pathway);ko04512(ECM-receptor interaction)
#> 2 ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hippo signaling pathway);ko04391(Hippo signaling pathway -fly);ko04013(MAPK signaling pathway - fly);ko04151(PI3K-Akt signaling pathway);ko04212(Longevity regulating pathway - worm)
#> 3 ko04610(Complement and coagulation cascades)
#> 4 ko04610(Complement and coagulation cascades)
#> 5 ko00970(Aminoacyl-tRNA biosynthesis)
#> 6 ko00250(Alanine, aspartate and glutamate metabolism);ko00280(Valine, leucine and isoleucine degradation);ko00650(Butanoate metabolism);ko00640(Propanoate metabolism);ko00410(beta-Alanine metabolism);ko04727(GABAergic synapse)
# 3. Default parameters
res <- table_cross(gene_expression2, gene_go_kegg, inter_var = "Genes")
head(res)
#> Genes CT_1 CT_2 CT_3 LT20_1 LT20_2 LT20_3 LT15_1 LT15_2 LT15_3 LT12_1
#> 1 14-3-3ZETA NA NA NA NA NA NA NA NA NA NA
#> 2 A1I3 NA NA NA NA NA NA NA NA NA NA
#> 3 A2M NA NA NA NA NA NA NA NA NA NA
#> 4 AARS NA NA NA NA NA NA NA NA NA NA
#> 5 ABAT NA NA NA NA NA NA NA NA NA NA
#> 6 ABCB7 NA NA NA NA NA NA NA NA NA NA
#> LT12_2 LT12_3 LT12_6_1 LT12_6_2 LT12_6_3
#> 1 NA NA NA NA NA
#> 2 NA NA NA NA NA
#> 3 NA NA NA NA NA
#> 4 NA NA NA NA NA
#> 5 NA NA NA NA NA
#> 6 NA NA NA NA NA
#> biological_process
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 GO:0006419(alanyl-tRNA aminoacylation)
#> 5 GO:0009448(gamma-aminobutyric acid metabolic process)
#> 6 <NA>
#> cellular_component
#> 1 <NA>
#> 2 GO:0005615(extracellular space)
#> 3 GO:0005615(extracellular space)
#> 4 GO:0005737(cytoplasm)
#> 5 <NA>
#> 6 GO:0016021(integral component of membrane)
#> molecular_function
#> 1 GO:0019904(protein domain specific binding)
#> 2 GO:0004866(endopeptidase inhibitor activity)
#> 3 GO:0004866(endopeptidase inhibitor activity)
#> 4 GO:0004813(alanine-tRNA ligase activity);GO:0005524(ATP binding);GO:0000049(tRNA binding);GO:0008270(zinc ion binding)
#> 5 GO:0003867(4-aminobutyrate transaminase activity);GO:0030170(pyridoxal phosphate binding)
#> 6 GO:0005524(ATP binding);GO:0016887(ATPase activity);GO:0042626(ATPase-coupled transmembrane transporter activity)
#> kegg_pathway
#> 1 ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hippo signaling pathway);ko04391(Hippo signaling pathway -fly);ko04013(MAPK signaling pathway - fly);ko04151(PI3K-Akt signaling pathway);ko04212(Longevity regulating pathway - worm)
#> 2 ko04610(Complement and coagulation cascades)
#> 3 ko04610(Complement and coagulation cascades)
#> 4 ko00970(Aminoacyl-tRNA biosynthesis)
#> 5 ko00250(Alanine, aspartate and glutamate metabolism);ko00280(Valine, leucine and isoleucine degradation);ko00650(Butanoate metabolism);ko00640(Propanoate metabolism);ko00410(beta-Alanine metabolism);ko04727(GABAergic synapse)
#> 6 ko02010(ABC transporters)
# 4. Set left_index = TRUE, right_index = FALSE
res <- table_cross(gene_expression2, gene_go_kegg,
inter_var = "Genes", left_index = TRUE, right_index = FALSE)
head(res)
#> Genes CT_1 CT_2 CT_3 LT20_1 LT20_2 LT20_3 LT15_1 LT15_2 LT15_3 LT12_1
#> 1 ACAA2 24.50 39.83 55.38 114.11 159.32 96.88 169.56 464.84 182.66 116.08
#> 2 ACAN 14.97 18.71 10.30 71.23 142.67 213.54 253.15 320.80 104.15 174.02
#> 3 ADH1 1.54 1.56 2.04 14.95 13.60 15.87 12.80 17.74 6.06 10.97
#> 4 AHSG 0.00 1911.99 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> 5 ALDH2 2.07 2.86 2.54 0.85 0.49 0.47 0.42 0.13 0.26 0.00
#> 6 AP1S3 6.62 14.59 9.30 24.90 33.94 23.19 24.00 36.08 27.40 24.06
#> LT12_2 LT12_3 LT12_6_1 LT12_6_2 LT12_6_3
#> 1 497.29 464.48 471.43 693.62 229.77
#> 2 305.81 469.48 1291.90 991.90 966.77
#> 3 10.71 30.95 9.84 10.91 7.28
#> 4 0.00 0.00 0.00 0.00 0.00
#> 5 0.28 0.11 0.37 0.15 0.11
#> 6 38.74 34.54 62.72 41.36 28.75
#> biological_process
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 GO:0006886(intracellular protein transport);GO:0016192(vesicle-mediated transport)
#> cellular_component
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 GO:0030117(membrane coat)
#> molecular_function
#> 1 GO:0016747(transferase activity, transferring acyl groups other than amino-acyl groups)
#> 2 <NA>
#> 3 GO:0016491(oxidoreductase activity);GO:0008270(zinc ion binding)
#> 4 <NA>
#> 5 GO:0016620(oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor)
#> 6 <NA>
#> kegg_pathway
#> 1 ko00280(Valine, leucine and isoleucine degradation);ko00071(Fatty acid degradation);ko00062(Fatty acid elongation);ko01212(Fatty acid metabolism)
#> 2 <NA>
#> 3 ko00350(Tyrosine metabolism);ko00010(Glycolysis / Gluconeogenesis);ko00680(Methane metabolism);ko00071(Fatty acid degradation);ko00830(Retinol metabolism);ko01200(Carbon metabolism);ko01220(Degradation of aromatic compounds);ko00625(Chloroalkane and chloroalkene degradation);ko00982(Drug metabolism - cytochrome P450);ko00980(Metabolism of xenobiotics by cytochrome P450);ko00626(Naphthalene degradation)
#> 4 <NA>
#> 5 ko00330(Arginine and proline metabolism);ko00340(Histidine metabolism);ko00310(Lysine degradation);ko00380(Tryptophan metabolism);ko00280(Valine, leucine and isoleucine degradation);ko00053(Ascorbate and aldarate metabolism);ko00010(Glycolysis / Gluconeogenesis);ko00620(Pyruvate metabolism);ko00071(Fatty acid degradation);ko00561(Glycerolipid metabolism);ko00410(beta-Alanine metabolism);ko00981(Insect hormone biosynthesis);ko00903(Limonene and pinene degradation);ko00625(Chloroalkane and chloroalkene degradation)
#> 6 ko04142(Lysosome)
# 5. Set left_index = FALSE, right_index = TRUE
res <- table_cross(gene_expression2, gene_go_kegg,
inter_var = "Genes", left_index = FALSE, right_index = TRUE)
head(res)
#> Genes CT_1 CT_2 CT_3 LT20_1 LT20_2 LT20_3 LT15_1 LT15_2 LT15_3 LT12_1
#> 1 14-3-3ZETA NA NA NA NA NA NA NA NA NA NA
#> 2 A1I3 NA NA NA NA NA NA NA NA NA NA
#> 3 A2M NA NA NA NA NA NA NA NA NA NA
#> 4 AARS NA NA NA NA NA NA NA NA NA NA
#> 5 ABAT NA NA NA NA NA NA NA NA NA NA
#> 6 ABCB7 NA NA NA NA NA NA NA NA NA NA
#> LT12_2 LT12_3 LT12_6_1 LT12_6_2 LT12_6_3
#> 1 NA NA NA NA NA
#> 2 NA NA NA NA NA
#> 3 NA NA NA NA NA
#> 4 NA NA NA NA NA
#> 5 NA NA NA NA NA
#> 6 NA NA NA NA NA
#> biological_process
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 GO:0006419(alanyl-tRNA aminoacylation)
#> 5 GO:0009448(gamma-aminobutyric acid metabolic process)
#> 6 <NA>
#> cellular_component
#> 1 <NA>
#> 2 GO:0005615(extracellular space)
#> 3 GO:0005615(extracellular space)
#> 4 GO:0005737(cytoplasm)
#> 5 <NA>
#> 6 GO:0016021(integral component of membrane)
#> molecular_function
#> 1 GO:0019904(protein domain specific binding)
#> 2 GO:0004866(endopeptidase inhibitor activity)
#> 3 GO:0004866(endopeptidase inhibitor activity)
#> 4 GO:0004813(alanine-tRNA ligase activity);GO:0005524(ATP binding);GO:0000049(tRNA binding);GO:0008270(zinc ion binding)
#> 5 GO:0003867(4-aminobutyrate transaminase activity);GO:0030170(pyridoxal phosphate binding)
#> 6 GO:0005524(ATP binding);GO:0016887(ATPase activity);GO:0042626(ATPase-coupled transmembrane transporter activity)
#> kegg_pathway
#> 1 ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hippo signaling pathway);ko04391(Hippo signaling pathway -fly);ko04013(MAPK signaling pathway - fly);ko04151(PI3K-Akt signaling pathway);ko04212(Longevity regulating pathway - worm)
#> 2 ko04610(Complement and coagulation cascades)
#> 3 ko04610(Complement and coagulation cascades)
#> 4 ko00970(Aminoacyl-tRNA biosynthesis)
#> 5 ko00250(Alanine, aspartate and glutamate metabolism);ko00280(Valine, leucine and isoleucine degradation);ko00650(Butanoate metabolism);ko00640(Propanoate metabolism);ko00410(beta-Alanine metabolism);ko04727(GABAergic synapse)
#> 6 ko02010(ABC transporters)