assemble_logfc_QC: assemble_logfc_QC

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

Description

Assembles logFC-based QC metrics.

Usage

assemble_logfc_QC(
  qc_metrics,
  screen_goal,
  lfc.ctrl_pl,
  lfc.treat_pl,
  lfc.ctrl_pl.repl,
  lfc.treat_pl.repl,
  library
)

Arguments

qc_metrics	A data frame containing only sequencing-based QC metrics (rows as samples, QC metrics as columns).
screen_goal	A character string naming the screen goal.
lfc.ctrl_pl	A data frame of gRNA logFC data for Control vs Plasmid (gRNAs as rows).
lfc.treat_pl	A data frame of gRNA logFC data for Treatment vs Plasmid (gRNAs as rows). Ignored, if 'NULL'.
lfc.ctrl_pl.repl	A data frame of gRNA logFC data for replicate-based Control vs Plasmid (gRNAs as rows).
lfc.treat_pl.repl	A data frame of gRNA logFC data for replicate-based Treatment vs Plasmid (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.

Value

A modified 'qc_metrics' data frame containing all logFC-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.