srx_agg: Summarized run data to experiments

Description Usage Arguments Value Examples

View source: R/getDEE2.R

Description

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

Usage

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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

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

markziemann/getDEE2 documentation built on Dec. 21, 2021, 2:48 p.m.