srx_agg_se: srx_agg_se is a version of srx_agg that works on...

In flaviusb/homosapienDEE2CellScore: Example Data Package for CellScore

srx_agg_se is a version of srx_agg that works on SummarizedExperiments

Description

This function aggregates runs that represent the same SRA experiment, and reorganises the coldata in the SummarizedExperiment to to be grouped by SRA experiment in order to preserve necessary SummarizedExperiment internal invariants.

Usage

srx_agg_se(x, counts = "GeneCounts")

Arguments

x	A SummarizedExperiment.
counts	What kind of count; "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 SummarizedExperiment object, with runs representing the same SRA experiment aggregated, and with coldata grouped by SRA experiment.

Examples

# This is a small SummarizedExperiment containing some un-aggregated data
small_data <- readInSEZip(
  system.file("ASmallSummarizedExperiment.zip", package="homosapienDEE2CellScore"))
# We can aggregate it like so:
aggregated_small_data <- srx_agg_se(small_data)

flaviusb/homosapienDEE2CellScore documentation built on April 11, 2024, 1:47 p.m.