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

Description Usage Arguments Details See Also Examples

View source: R/conduct.R

Description

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

Usage

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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

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