fetch_expression: Retrieve expression data for genes/transcripts across samples

In denalitherapeutics/archs4: Wrappers to query and extract ARCHS4 data

Description

Returns the estimated counts for the genes/transcripts enumerated in the features table for the samples enumerated in the samples table.

Usage

fetch_expression(a4, features, samples = NULL, feature_type = "gene",
  source = NULL, feature_meta = "symbol",
  sample_meta = c("Sample_title", "Sample_source_name_ch1"),
  prior.count = 3, ...)

Arguments

a4	An Archs4Repository
features	a tibble of feature descriptors (as returned from feature_info()). Really this table simply needs the following columns: "a4name" or "ensembl_id" or; "feature_type": (gene or transcript) "source" (human or mouse),;
samples	a samples identifier: ie. a tibble with series_id and sample_id columns.
source	"mouse" or "human" pass this in explicitly if there is no "source" column in your features or samples data.frame
feature_meta	additional columns from feature_info(a4, feature_type = feature_type)
sample_meta	metadata information to include for the samples. These values are extracted from the meta/VALUE files in the respective hdf5 data files. See archs4_sample_info() for more details.
type	"gene" or "transcript"-level data?

Details

Note that the values returned are simply estimated counts. They are not normalized by sequencing depth. For now, the only use for this function is to compare how ratios of genes compare across samples.

Value

a data.frame of expression data. Each row is an observation (one gene one sample)

See Also

as.DGEList()

Examples

a4 <- Archs4Repository()
gnz <- feature_lookup(a4, c("CFAP65", "PECR"))
gexprs <- fetch_expression(a4, gnz)

denalitherapeutics/archs4 documentation built on May 17, 2019, 1:29 p.m.