Check to see that samples are referenced correctly

Source: R/validation.R

Samples have compound keys: dataset,sample_id. If we want to index into them, we can either:

assert_sample_subset(x, fds = NULL, ..., .var.name = vname(x), add = NULL)

check_sample_subset(x, fds = NULL, ...)

test_sample_subset(x, fds = NULL, ...)

assert_facet_descriptor(x)

is_facet_descriptor(x)

assert_assay_feature_descriptor(x, .fds = NULL)

is_assay_feature_descriptor(x, .fds = NULL)

assert_expression_result(x)

is_expression_result(x)

assert_sample_statistics(x)

is_sample_statistics(x)

assert_sample_covariates(x)

is_sample_covariates(x)

assert_columns(x, req.cols)

has_columns(x, req.cols, warn = TRUE)

assert_covariate_definitions(x, required = NULL)

is_covariate_definitions(x, required = NULL)

Details

  1. pass a data.frame around with dataset and sample_id columns

  2. pass a "loaded up" tbl_sqlite" over the sample_covariate table which has your filters of interest set

assay_feature_descriptor

If .fds is provided, it must be a FaclieDataSet and these functions will check to ensure that the x[['assay']] is a valid assay element in .fds