sample-covariates: Appends covariate columns to a query result

In facilebio/FacileData: A fluent API for accessing multi-assay high-throughput genomics data

Appends covariate columns to a query result

Description

Note that this function will force the collection of x

Usage

fetch_sample_covariates(
  x,
  covariates = NULL,
  samples = NULL,
  custom_key = Sys.getenv("USER"),
  with_source = FALSE,
  ...
)

with_sample_covariates(
  x,
  covariates = NULL,
  na.rm = FALSE,
  custom_key = Sys.getenv("USER"),
  .fds = NULL,
  ...
)

## S3 method for class 'FacileDataSet'
fetch_sample_covariates(
  x,
  covariates = NULL,
  samples = NULL,
  custom_key = Sys.getenv("USER"),
  with_source = FALSE,
  ...
)

## S3 method for class 'facile_frame'
fetch_sample_covariates(
  x,
  covariates = NULL,
  samples = NULL,
  custom_key = Sys.getenv("USER"),
  with_source = FALSE,
  ...
)

Arguments

x	a FacileDataSet connection
covariates	character vector of covariate names
samples	a samples descriptor tbl_*
custom_key	The key to use to fetch more custom annotations over the given samples
na.rm	if TRUE, filters outgoing result such that only rows with nonNA values for the covariates specified here will be returned. Default: FALSE. Note that this will not check columns not specified in covariates for NA-ness.
.fds	A FacileDataSet object

Value

The facile x object, annotated with the specified covariates.

rows from the sample_covariate table

See Also

Other FacileInterface: facet_frame.FacileDataSet(), fetch_assay_score(), fetch_sample_statistics(), samples()

Other API: fetch_assay_score.FacileDataSet(), fetch_custom_sample_covariates.FacileDataSet(), fetch_sample_statistics.FacileDataSet(), fetch_samples.FacileDataSet(), filter_features.FacileDataSet(), filter_samples.FacileDataSet(), organism.FacileDataSet(), samples.FacileDataSet()

Other FacileInterface: facet_frame.FacileDataSet(), fetch_assay_score(), fetch_sample_statistics(), samples()

Other API: fetch_assay_score.FacileDataSet(), fetch_custom_sample_covariates.FacileDataSet(), fetch_sample_statistics.FacileDataSet(), fetch_samples.FacileDataSet(), filter_features.FacileDataSet(), filter_samples.FacileDataSet(), organism.FacileDataSet(), samples.FacileDataSet()

Other API: fetch_assay_score.FacileDataSet(), fetch_custom_sample_covariates.FacileDataSet(), fetch_sample_statistics.FacileDataSet(), fetch_samples.FacileDataSet(), filter_features.FacileDataSet(), filter_samples.FacileDataSet(), organism.FacileDataSet(), samples.FacileDataSet()

Examples

# Retrieves a long EAV table of covariates
long_covs <- an_fds() |> 
  fetch_sample_covariates(c("cell_abbrev", "sex", "condition"))
lc2 <- some_samples() |> 
  fetch_sample_covariates(c("cell_abbrev", "sex", "condition"))
wide_covs <- some_samples() |> 
  with_sample_covariates(c("cell_abbrev", "sex", "condition"))

facilebio/FacileData documentation built on Feb. 23, 2024, 9:14 a.m.