tomo_quality: Tomosequencing quality control function

In erikschild/TomoQC: Simple QC for tomo-seq

Description

Tomosequencing quality control function

Usage

tomo_quality(
  transcripts = example_data$transcripts,
  reads = example_data$reads,
  umis = example_data$UMIs,
  plot_title = "QC plots",
  cutoff_spike = 25,
  cutoff_genes = 100,
  spike_ins = T
)

Arguments

transcripts	data.frame containing transcript counts, with gene names in the first column
reads	data.frame containing read counts, with gene names in the first column
umis	data.frame containing UMI counts, with genen names in the first column
plot_title	a string to title the QC plot
cutoff_spike	a cutoff value for spike-in percentage of total Transcripts (ranges from 0 to 100)
cutoff_genes	a cutoff value for minimum unique gene count per slice
spike_ins	Controls whether spike-ins were used, and thus if a spike-ins percentage plot should be generated. Default = TRUE

Value

Provides various QC plots to quickly assess the quality of tomo-seq data

erikschild/TomoQC documentation built on Jan. 9, 2021, 12:36 a.m.