Read in trabecular bone data — read_trabecular

These are wrappers around readr::read_csv() and readxl::read_excel() to read in and process trabecular bone microCT data from a trabecular.csv file or the Trabecular sheet of a data.xlsx file. It uses a key object to look up and add sex, genotype, and site information.

Usage

read_trabecular_csv(file, key, ...)

read_trabecular_excel(file, key, sheet = "Trabecular", ...)

Arguments

file: The file path to the trabecular.csv or data.xlsx file.
key: The key object containing sample information, as created by the read_key_csv() or read_key_excel() function.
...: Additional arguments passed on to readr::read_csv() or readxl::read_excel().
sheet: For read_trabecular_excel(), the sheet to read. Either a string (the name of a sheet), or an integer (the position of the sheet). Defaults to "Trabecular".

Value

A tibble/data frame containing trabecular bone data. For example:

|   AS|Sex |Genotype | SampNo|Site  | MeasNo| BV/TV|   SMI|   Tb.N| Tb.Th| Tb.Sp|
|----:|:---|:--------|------:|:-----|------:|-----:|-----:|------:|-----:|-----:|
| 1365|M   |Cre      |  10778|Spine |  31711| 13.05| 1.631|  3.097| 0.051| 0.316|
| 1365|M   |Cre      |  10778|Met   |  31710|  5.43| 3.227|  2.460| 0.062| 0.412|
| 1366|F   |Cre      |  10779|Spine |  31714| 21.88| 0.987| 14.227| 0.047| 0.111|
| 1366|F   |Cre      |  10779|Met   |  31713|  4.47| 3.725|  2.666| 0.059| 0.371|
| 1367|F   |Cre;fl   |  10780|Spine |  31717| 14.47| 0.989|  2.551| 0.060| 0.398|
| 1367|F   |Cre;fl   |  10780|Met   |  31716|  0.23| 4.172|  1.789| 0.034| 0.558|

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_trab <- read_trabecular_csv(mctr_ex("example-trabecular.csv"),
                                        key = gen_key)
#> Rows: 24 Columns: 75
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (19): SampName, MeasDate, ListDate, Filename, Site, Energy-I-Code, Contr...
#> dbl (51): SampNo, MeasNo, Integr.Time, Sigma, Support, Threshold, Unit, Data...
#> lgl  (5): S-DOB, S-Remark, Meas-Rmk, RAW-Label, IMA-Label
#> 
#> 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_trab <- read_trabecular_excel(mctr_ex("example-genotype.xlsx"),
                                          key = gen_key)