srx_agg: Summarized run data to experiments

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

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 Dec. 21, 2021, 2:48 p.m.