Table split used for splitting a grouped column to multiple columns.
Source:R/table_split.R
table_split.RdTable split used for splitting a grouped column to multiple columns.
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).
- grouped_var
Character: grouped column name. Default: "go_category".
- value_var
Character: value column name. Default: "go_term".
- miss_drop
Logical: drop missing values or NA values. Default: TRUE, options: TRUE, FALSE.
Examples
# 1. Library TOmicsVis package
library(TOmicsVis)
# 2. Use example dataset
data(gene_go_kegg2)
head(gene_go_kegg2)
#> Genes
#> 1 FN1
#> 2 14-3-3ZETA
#> 3 A1I3
#> 4 A2M
#> 5 AARS
#> 6 ABAT
#> 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)
#> go_category
#> 1 biological_process
#> 2 biological_process
#> 3 biological_process
#> 4 biological_process
#> 5 biological_process
#> 6 biological_process
#> go_term
#> 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)
# 3. Default parameters
res <- table_split(gene_go_kegg2)
head(res)
#> Genes
#> 1 14-3-3ZETA
#> 2 A1I3
#> 3 A2M
#> 4 AARS
#> 5 ABAT
#> 6 ABCB7
#> 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)
#> 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)