.read_metabolon {autonomics} | R Documentation |
Read metabolon
.read_metabolon( file, sheet = "OrigScale", fid_var = "(COMP|COMP_ID)", sid_var = "(CLIENT_IDENTIFIER|Client ID)", sfile = NULL, sfileby = NULL, by = NULL, subgroupvar = "Group" ) read_metabolon( file, sheet = "OrigScale", fid_var = "(COMP|COMP_ID)", sid_var = "(CLIENT_IDENTIFIER|Client ID)", sfile = NULL, sfileby = NULL, by = NULL, subgroupvar = "Group", fname_var = "BIOCHEMICAL", impute = FALSE, add_kegg_pathways = FALSE, add_smiles = FALSE, pca = FALSE, fit = NULL, formula = NULL, block = NULL, contrastdefs = NULL, verbose = TRUE, plot = TRUE )
file |
metabolon xlsx filepath |
sheet |
xls sheet number or name |
fid_var |
feature_id fvar |
sid_var |
sampleid svar |
sfile |
sample file |
sfileby |
sample file mergeby column |
by |
metabolon file mergeby column |
subgroupvar |
subgroup svar |
fname_var |
featurename fvar |
impute |
whether to impute |
add_kegg_pathways |
whether to add kegg pathways |
add_smiles |
whether to add smiles |
pca |
whether to pca |
fit |
fit model: NULL, 'limma', 'lm', 'lme', 'lmer', 'wilcoxon' |
formula |
designmat formula |
block |
block svar |
contrastdefs |
contrastdef vector/matrix/list |
verbose |
whether to msg |
plot |
whether to plot |
SummarizedExperiment
file <- download_data('atkin18.metabolon.xlsx') read_metabolon(file, pca = TRUE, fit = 'limma', block='SUB')