srx_agg: Summarized run data to experiments

In markziemann/getDEE2: Programmatic access to the DEE2 RNA expression dataset

Summarized run data to experiments

Description

Sometimes, each SRA experiment data is represented in two or more runs and they need to be aggregated.

Usage

srx_agg(x, counts = "GeneCounts")

Arguments

x	a getDEE2 object.
counts	select "GeneCounts" for STAR based gene counts, "TxCounts" for kallisto transcript level counts or "Tx2Gene" for transcript counts aggregated to gene level. Default is "GeneCounts"

Value

a dataframe with gene expression data summarised to SRA experiment accession numbers rather than run accession numbers.

Examples

x <- getDEE2("ecoli",c("SRR1613487","SRR1613488"),legacy=TRUE)
y <- srx_agg(x)

markziemann/getDEE2 documentation built on Jan. 16, 2025, midnight