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Read in cortical bone data

read_cortical_csv.Rd

These are wrappers around readr::read_csv() and readxl::read_excel() to read in and process cortical bone microCT data from two files: a twice1.csv and a twice2.csv file, or the Twice1 and Twice2 sheets of a data.xlsx file. It uses a key object to look up and add sex, genotype, and site information.

Usage

read_cortical_csv(twice1_file, twice2_file, key, ...)

read_cortical_excel(
  data_file,
  key,
  twice1_sheet = "Twice1",
  twice2_sheet = "Twice2",
  ...
)

Arguments

twice1_file

The file path to the twice1.csv file (for read_cortical_csv()).

twice2_file

The file path to the twice2.csv file (for read_cortical_csv()).

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().

data_file

The path to the data.xlsx file (for read_cortical_excel()).

twice1_sheet, twice2_sheet

For read_cortical_excel(), the sheets to read. Either strings (the name of the sheets), or integers (the positions of the sheets). Default to "Twice1" and "Twice2".

Value

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

|   AS|Sex |Genotype | SampNo|Site | MeasNo|  Ct.vBMD| Ct.Th| End.Circ| Peri.Circ| Ct.Po| Ct.Po.V|
|----:|:---|:--------|------:|:----|------:|--------:|-----:|--------:|---------:|-----:|-------:|
| 1365|M   |Cre      |  10778|Met  |  31710|  937.049| 0.129|    5.533|     6.342|  0.41|   0.002|
| 1365|M   |Cre      |  10778|Dia  |  31712| 1114.873| 0.220|    3.963|     5.343|  0.11|   0.001|
| 1366|F   |Cre      |  10779|Met  |  31713| 1011.473| 0.183|    4.337|     5.485|  0.26|   0.001|
| 1366|F   |Cre      |  10779|Dia  |  31715| 1133.066| 0.232|    3.250|     4.705|  0.10|   0.000|
| 1367|F   |Cre;fl   |  10780|Met  |  31716|  994.868| 0.145|    4.892|     5.806|  0.37|   0.002|
| 1367|F   |Cre;fl   |  10780|Dia  |  31718| 1137.300| 0.209|    3.514|     4.827|  0.14|   0.001|

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_cort <- read_cortical_csv(mctr_ex("example-twice1.csv"),
                              mctr_ex("example-twice2.csv"),
                              gen_key)
#> Rows: 36 Columns: 75
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (44): SampName, MeasDate, ListDate, Filename, Site, Energy-I-Code, Contr...
#> dbl (26): 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.
#> Rows: 36 Columns: 75
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (43): SampName, MeasDate, ListDate, Filename, Site, Energy-I-Code, Contr...
#> dbl (27): 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_cort <- read_cortical_excel(mctr_ex("example-genotype.xlsx"),
                                gen_key)