assemble_counts_QC: assemble_counts_QC

In alex-kalinka-cruk/fgcQC: QC metric calculations for CRISPR screen data produced at the FGC

Description

Assembles counts-based QC metrics.

Usage

assemble_counts_QC(
  qc_metrics,
  counts,
  counts_norm,
  library,
  plasmid_samp,
  control_samp,
  treat_samp
)

Arguments

qc_metrics	A data frame containing only sequencing-based QC metrics (rows as samples, QC metrics as columns).
counts	A data frame of counts for each sample in the study (samples as columns, gRNAs as rows).
counts_norm	A data frame of normalized counts for each sample in the study (samples as columns, gRNAs as rows).
library	A data frame containing the library file in which the first column gives the sgRNA sequence and the second column gives the sgRNA ID.
plasmid_samp	A character vector naming one or more plasmid samples.
control_samp	A character vector naming one or more control samples.
treat_samp	A character vector naming one or more treatment samples. If 'NULL' then there are no treatment samples.

Value

A modified 'qc_metrics' data frame containing all counts-based QC metrics (both experiment and sample-level).

Author(s)

Alex T. Kalinka, [e-mail]

alex-kalinka-cruk/fgcQC documentation built on June 23, 2020, 9:05 p.m.