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Creates a CAN_data object

Source: R/input_data_constructors.R
CAN_data.Rd

Creates a CAN_data object from a tibble or data-frame of candidate genes.

Usage

CAN_data(dat, keep_rownames_as = NULL)

Arguments

dat

Tibble, set of candidate genes of interest. See Details.

keep_rownames_as

Character, the name of the column in which to save the rownames of the input data-frame. Default value is NULL, i.e. rownames will be discarded.

Value

A CAN_data object, i.e. a tibble.

Details

The input data should have one row per gene, and at least the following columns:

  • chromosome: character column, chromosome on which the gene is located.

  • start and end: numeric, starting and end position of the gene (in bp). A column position will be constructed as the middle value (mean) between start and end.

  • name: character, the name of the candidate genes to be displayed.

Examples

x <- get_example_data()

CAN_data(x[["CAN"]])
#> # A tibble: 32 × 7
#>    id                    chromosome    start      end name    gene_name position
#>    <chr>                 <chr>         <dbl>    <dbl> <chr>   <chr>        <dbl>
#>  1 PGSC0003DMG400003155  ST4.03ch03 46757152 46762127 4CL     4-coumar…   4.68e7
#>  2 PGSC0003DMG400014223  ST4.03ch03 57466692 57469946 4CL2    4-coumar…   5.75e7
#>  3 PGSC0003DMG400011189  ST4.03ch07  1001854  1006278 HQT     HQT         1.00e6
#>  4 PGSC0003DMG400005492  ST4.03ch05 36342746 36347409 PAL     phenylal…   3.63e7
#>  5 PGSC0003DMG400005279  ST4.03ch05 42523943 42525912 peroxi… peroxida…   4.25e7
#>  6 PGSC0003DMG400007782  ST4.03ch03 38537202 38540209 PHO1A   PHO1A       3.85e7
#>  7 PGSC0003DMG400023182  ST4.03ch02 10091564 10093164 LIPIII… LipIII27    1.01e7
#>  8 PGSC0003DMG400029576  ST4.03ch08 45676042 45677832 PPOs    Polyphen…   4.57e7
#>  9 PGSC0003DMG400018924  ST4.03ch08 45778567 45780333 NA      Polyphen…   4.58e7
#> 10 PGSC0003DMG400018919  ST4.03ch08 45793661 45794229 NA      Polyphen…   4.58e7
#> # ℹ 22 more rows