brucemoran_rnaseq_kallisto_parser: Take metadata CSV, parse Kallisto output and return a Sleuth...

In brucemoran/RNAseqR: RNAseq DE Analysis Downstream from Nextflow Pipelines

Description

Take metadata CSV, parse Kallisto output and return a Sleuth object with raw counts

Usage

brucemoran_rnaseq_kallisto_parser(
  metadata_csv,
  data_dir = NULL,
  agg_col = "ensembl_gene_id",
  genome_prefix = "hsapiens",
  server_threads = NULL
)

Arguments

metadata_csv	CSV format file with columns: 'sample' that has exact dir matching which contains 'adundance.h5' (recursively)
data_dir	dir from which to recursively search for abundance.h5 for samples
agg_col	column on which to aggregate gene_mode
genome_prefix	string of a genome in biomart$dataset, suffixed with '_gene_ensembl'
server_threads	set to anything but NULL to allow threading

Value

list object with sleuth object 'so' [1] and tx2gene annotation used to create it [2]

brucemoran/RNAseqR documentation built on Sept. 14, 2021, 11:08 a.m.