microCTr

This packages contains functions to read in and analyze microCT data as currently performed in the Khosla Lab. Data come from a Scanco vivaCT 40. Sites analyzed include femoral metaphysis, femoral diaphysis, and lumbar vertebra. Analyses include trabecular bone parameters, cortical bone parameters, and finite element analysis.

Installation

You can install the development version of microCTr from GitHub with:

# install.packages("remotes")
remotes::install_github("ricompute/microCTr")

Example

Please see the package website for details and more examples, including a vignette showing a complete analysis comparing two genotypes.

library(microCTr)

key <- read_key_excel(mctr_ex("example-genotype.xlsx"))

trab <- read_trabecular_excel(mctr_ex("example-genotype.xlsx"), key)

F.Met.Trab <- trab |> dplyr::filter(Site == "Met") |> compare_groups()

print_results(F.Met.Trab)

BV/TV

Sex	Genotype	n	Mean	SEM	P	Sig
M	Cre	3	6.82	0.954
M	Cre;fl	3	11.27	2.427	0.163

SMI

Sex	Genotype	n	Mean	SEM	P	Sig
M	Cre	3	3.06	0.084
M	Cre;fl	3	2.54	0.464	0.33

Tb.N

Sex	Genotype	n	Mean	SEM	P	Sig
M	Cre	3	2.62	0.103
M	Cre;fl	3	3.08	0.203	0.116

Tb.Th

Sex	Genotype	n	Mean	SEM	P	Sig
M	Cre	3	0.065	0.004
M	Cre;fl	3	0.069	0.002	0.323

Tb.Sp

Sex	Genotype	n	Mean	SEM	P	Sig
M	Cre	3	0.379	0.018
M	Cre;fl	3	0.314	0.020	0.074

BV/TV

Sex	Genotype	n	Mean	SEM	P	Sig
F	Cre	3	2.690	0.930
F	Cre;fl	3	0.873	0.405	0.148

SMI

Sex	Genotype	n	Mean	SEM	P	Sig
F	Cre	3	3.83	0.306
F	Cre;fl	3	3.90	0.233	0.871

Tb.N

Sex	Genotype	n	Mean	SEM	P	Sig
F	Cre	3	2.30	0.375
F	Cre;fl	3	1.92	0.092	0.375

Tb.Th

Sex	Genotype	n	Mean	SEM	P	Sig
F	Cre	3	0.056	0.011
F	Cre;fl	3	0.037	0.002	0.167

Tb.Sp

Sex	Genotype	n	Mean	SEM	P	Sig
F	Cre	3	0.470	0.098
F	Cre;fl	3	0.522	0.022	0.627