as.DGEList: Create a DGEList for the expression data of a series or set...

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

Description

Create a DGEList for the expression data of a series or set of samples.

Usage

as.DGEList(x, id, features = NULL, sample_columns = c("Sample_title",
  "Sample_source_name_ch1"), feature_type = c("gene", "transcript"),
  row_id = c("ensembl", "symbol"), check_missing_samples = TRUE)

Arguments

id	a vector of series or sample id's.
features	a feature-descriptor of the features you want to include counts for
sample_columns	the names of the sample covariates that are stored in the ARCHS4 Dataset; a complete list of what covariates are available in the ARCHS4 dataset is found using the archs4_sample_covariates() function.
feature_type	do you want "gene" or "transcript" level expression?
row_id	either "ensembl" or "symbol". If this is "ensembl" and feature_type == "transcript", then we remove the rows from the count dataset that we couldn't map symbol -> ensembl_gene_id for.

Value

a DGEList of results

See Also

fetch_expression()

Examples

a4 <- Archs4Repository()
y <- as.DGEList(a4, "GSE89189", feature_type = "gene")

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