load_archs4_seq: Load ExpressionSet from ARCHS4 h5 file

In alexvpickering/rkal: Run, Import, and Export 'kallisto' Quantifications

Load ExpressionSet from ARCHS4 h5 file

Description

ARCHS4 h5 files are available at https://maayanlab.cloud/archs4/download.html

Usage

load_archs4_seq(
  archs4_file,
  gsm_names,
  species = "Homo sapiens",
  release = "94",
  load_saved = TRUE,
  eset_path = NULL
)

Arguments

archs4_file	Path to human_matrix.h5 file.
gsm_names	Character vector of GSM names of samples to load.
species	Character vector indicating species. Genus and species should be space separated, not underscore. Default is Homo sapiens.
release	EnsemblDB release. Should be same as used in build_kallisto_index.
load_saved	Should a previously saved eset be loaded? Requires eset_path to be specified.
eset_path	Path to load saved eset from or to save eset to.

Value

ExpressionSet

Examples

archs4_file <- "/path/to/human_matrix_v*.h5"
gsm_names <- c("GSM3190508", "GSM3190509", "GSM3190510", "GSM3190511")
# eset <- load_archs4_seq(archs4_file, gsm_names)

alexvpickering/rkal documentation built on Nov. 27, 2022, 8:38 p.m.