conduct: Conduct: Single-function processing of CRISPR screen data

In christensensm/COMPOSE: Calculation and Visualization of Phenotypic CRISPR Screens

Description

This function ties together all the basics of the COMPOSE package to give you a one-stop shop for processing data.

Usage

conduct(
  counts = NULL,
  metadata = NULL,
  sample.id = "SampleID",
  save.plot = T,
  save.table = T,
  identifier1 = NULL,
  identifier2 = NULL,
  identifier3 = NULL,
  batch = F,
  batch.id = NULL,
  transform = T,
  cpm = T,
  thresh = 1,
  minsample.ids = 2,
  meta.idnum = NULL,
  cutoff = 0.5,
  sig.cutoff = 0.05,
  verbose = T,
  top.labels = 30,
  neg.controls = NULL,
  essential.genes = NULL,
  split = "_",
  list.return = T,
  pathway.analysis = F,
  gene.db = NULL
)

Arguments

counts	input matrix containing normalized gRNA counts with gRNA ids as row names
metadata	input dataframe containing sample names and other identifiers or data including batch, treatments, etc.
sample.id	string identifying column name in metadata containing sample IDs
save.plot	logical - save the plot to pdf or print to screen (default saves everything to one pdf)
save.table	logical - save the tables (default saves everything)
identifier1	string identifying column name of metadata with which to adjust color in PCA plot
identifier2	string identifying column name of metadata with which to adjust size in PCA plot
identifier3	string identifying column name of metadata with which to adjust shape in PCA plot
batch	logical - correct for batch effects (requires a batch.id input)
batch.id	numerical - column of metadata that identifies the batch effect to remove
transform	logical - do you want to log10 transform the counts
cpm	logical - do you want to normalize the counts by sequencing depth
thresh	numerical cutoff for low counts
minsample.ids	minimum number of samples for which counts must be present per gene
meta.idnum	vector containing the column numbers in metadata that represent (1) Cell line, (2) replicates, and (3) condition
cutoff	gene score cutoff for comparisons between contrasts (default = 1)
sig.cutoff	numeric - specified p-value cut-off
verbose	TRUE/FALSE (default = TRUE)
top.labels	numerical - number of top guides to label (by p-value)
neg.controls	input vector containing gRNA ids for negative controls
essential.genes	input vector containing gRNA ids for essential genes
split	defines the regex used to split the guide RNA id to extract the gene name
list.return	logical - return a list containing gene names for every intersection
pathway.analysis	(TRUE/FALSE) continue with pathway analysis for all contrasts
gene.db	genome database from which to convert gene symbols to other ids

Details

The required arguments to run the simplest analysis include counts, metadata, meta.idnum, essential.genes, and neg.controls (if pathway.analysis = F).

See Also

COMPOSE the COMPOSE package

Examples

...

christensensm/COMPOSE documentation built on Dec. 22, 2020, 3:43 a.m.