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Create sets of buttons for gene symbols

Source: R/buttonifier.R
buttonifier.Rd

A function to turn Gene Symbols into buttons in an Rmarkdown linking to various portals for further info about these genes.

Usage

buttonifier(
  df,
  create_buttons_to = c("PUBMED", "GC", "UNIPROT"),
  col_to_use = "SYMBOL",
  output_format = "DT",
  ens_col = NULL,
  ens_species = NULL
)

Arguments

df

A dataframe with at least on column with gene Symbols named: SYMBOL

create_buttons_to

At least one of: "GC", "NCBI", "GTEX", "UNIPROT", "dbPTM", "HPA" "PUBMED"

col_to_use

name of the columns were the gene symbols are stored. Default is SYMBOL

output_format

a parameter deciding which output format to return, either a "DT" (DT::datatable(), recommended), or a simple dataframe ("DF"). In the latter case it is important that if the data is visualized with the DT::datatable function the parameter escape must be set to FALSE

ens_col

Character string, name of the columns were the ENSEMBL IDs are stored.

ens_species

The species you are working with to link to the correct gene on ENSEMBL

Value

A data.frame or a DT::datatable object with columns adding HTML objects that link to websites with further information on the genes in question.

Details

Current supported portals are: GeneCards, NCBI, GTEx, Uniprot, dbPTM, Human Protein Atlas

Examples

data(res_de_macrophage, package = "mosdef")

res_de <- res_macrophage_IFNg_vs_naive
res_df <- deresult_to_df(res_de)
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead

## Subsetting for quicker run
res_df <- res_df[1:100, ]
buttonifier(res_df)



buttonifier(res_df,
  create_buttons_to = c("NCBI", "HPA"),
  ens_col = "id",
  ens_species = "Homo_sapiens"
)