Read in a sample definition key file — read_key

These are wrappers around readr::read_csv() and readxl::read_excel() to read in and process a key.csv file or Key sheet of a data.xlsx file that contains the lookup table defining each sample's AS (key registry) number, sex, genotype (if applicable), treatment (if applicable), sample number, and the measure number of each site scanned.

Usage

read_key_csv(file, sites = c("Spine", "Met", "Dia"), ...)

read_key_excel(file, sites = c("Spine", "Met", "Dia"), sheet = "Key", ...)

Arguments

file: The file path to the key.csv or data.xlsx file.
sites: A character vector of the sites scanned, included as columns in the key file.
...: Additional arguments passed on to readr::read_csv() or readxl::read_excel().
sheet: For read_key_excel(), the sheet to read. Either a string (the name of a sheet), or an integer (the position of the sheet). Defaults to "Key".

Value

A tibble/data frame containing the sample definitions. For example:

|   AS|Sex |Genotype | SampNo|Site  | MeasNo|
|----:|:---|:--------|------:|:-----|------:|
| 1365|M   |Cre      |  10778|Spine |  31711|
| 1365|M   |Cre      |  10778|Met   |  31710|
| 1365|M   |Cre      |  10778|Dia   |  31712|
| 1366|F   |Cre      |  10779|Spine |  31714|
| 1366|F   |Cre      |  10779|Met   |  31713|
| 1366|F   |Cre      |  10779|Dia   |  31715|

Examples

gen_key <- read_key_csv(mctr_ex("example-gen-key.csv"))
#> Rows: 12 Columns: 7
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (2): Sex, Genotype
#> dbl (5): AS, SampNo, Spine, Met, Dia
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
gen_key <- read_key_excel(mctr_ex("example-genotype.xlsx"))