get_quant_meta: Transform GEO metadata for quantification

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

Transform GEO metadata for quantification

Description

Transform GEO metadata for quantification

Usage

get_quant_meta(srp_meta, data_dir)

Arguments

srp_meta	data.frame of GEO metadata from crawl_gsms
data_dir	Directory with raw fastq.gz RNA-Seq files.

Value

data.frame needed for parameter quant_meta in run_kallisto_bulk

Examples

# example srp_meta
srp_meta <- data.frame(
    run = "SRR1",
    gsm_name = "GSM4875733",
    library_layout = "PAIRED"
)

# example paired fastq files
data_dir <- tempdir()
file.create(file.path(data_dir, c("SRR1_1.fastq.gz", "SRR1_2.fastq.gz")))
quant_meta <- get_quant_meta(srp_meta, data_dir)

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