Table merge used to merge multiple variables to on variable.
Usage
table_merge(
data,
merge_vars = c("biological_process", "cellular_component", "molecular_function"),
new_var = "go_category",
new_value = "go_term",
na_remove = FALSE
)Arguments
- data
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).
- merge_vars
Vector: include merged variable (column) names. Default: c("Ozone", "Solar.R", "Wind", "Temp") in example data.
- new_var
Character: new variable (column) name. Default: "Variable".
- new_value
Character: new variable (column) value name. Default: "Value".
- na_remove
Logical: remove NA value. Default: FALSE, options: TRUE, FALSE.
Examples
# 1. Library TOmicsVis package
library(TOmicsVis)
# 2. Use example dataset
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_merge(gene_go_kegg)
head(res)
#> # A tibble: 6 × 4
#> Genes kegg_pathway go_category go_term
#> <chr> <chr> <chr> <chr>
#> 1 FN1 ko04810(Regulation of actin cytoskeleton);ko04… biological… GO:000…
#> 2 FN1 ko04810(Regulation of actin cytoskeleton);ko04… cellular_c… GO:000…
#> 3 FN1 ko04810(Regulation of actin cytoskeleton);ko04… molecular_… NA
#> 4 14-3-3ZETA ko04110(Cell cycle);ko04114(Oocyte meiosis);ko… biological… NA
#> 5 14-3-3ZETA ko04110(Cell cycle);ko04114(Oocyte meiosis);ko… cellular_c… NA
#> 6 14-3-3ZETA ko04110(Cell cycle);ko04114(Oocyte meiosis);ko… molecular_… GO:001…
# 4. Set new_var = "GO", new_value = "Terms"
res <- table_merge(gene_go_kegg, new_var = "GO", new_value = "Terms")
head(res)
#> # A tibble: 6 × 4
#> Genes kegg_pathway GO Terms
#> <chr> <chr> <chr> <chr>
#> 1 FN1 ko04810(Regulation of actin cytoskeleton);ko04510(Foca… biol… GO:0…
#> 2 FN1 ko04810(Regulation of actin cytoskeleton);ko04510(Foca… cell… GO:0…
#> 3 FN1 ko04810(Regulation of actin cytoskeleton);ko04510(Foca… mole… NA
#> 4 14-3-3ZETA ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hi… biol… NA
#> 5 14-3-3ZETA ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hi… cell… NA
#> 6 14-3-3ZETA ko04110(Cell cycle);ko04114(Oocyte meiosis);ko04390(Hi… mole… GO:0…