ct.seasPrep: Prepare one or more resultsDF objects for analysis via...

In OscarBrock/gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Prepare one or more resultsDF objects for analysis via Sparrow.

Description

Take in a list of results objects and return an equivalently-named list of input 'data.frames' appropriate for 'sparrow::seas()'. By construction, the relevant target unit is extracted from the 'geneSymbol' column of the provided results objects, which may. Note that the genewise '@logFC' slot in the returned object will contain the appropriately-signed Z transformation of the P-value assigned to the target. In most applications this is arguably more interpretable than e.g., the median gRNA log2 fold change.

Usage

ct.seasPrep(
  dflist,
  collapse.on = c("geneID", "geneSymbol"),
  cutoff = 0.1,
  statistic = c("best.q", "best.p"),
  regularize = FALSE,
  gdb = NULL,
  active = "replicated"
)

Arguments

dflist	A list of gCrisprTools results 'data.frames' to be formatted.
collapse.on	Should targets be annotated as 'geneSymbol's or 'geneID's (default)?
cutoff	Numeric maximum value of 'statistic' to define significance.
statistic	Should cutoffs be calculated based on FDR ('best.q') or P-value ('best.p')?
regularize	Logical indicating whether to regularize the result objects in 'dflist' (e.g., use intersection set of all targets), or keep as-is.
gdb	Optionally, a 'GeneSetDb' object to enable proper registration of the output. If provided, the collapsing features in the provided 'simpleDF's must be present in the 'gsd@db$feature_id' slot. Note that a GREAT-style 'GeneSetDb' that has been conformed via 'ct.GREATdb()' will use 'geneID's as the 'feature_id'.
active	Optionally, the name of a logical column present in the provided result that will be used to define significant signals. This is set to 'replicated' by default to If a valid column name is provided, this overrides the specification of 'cutoff' and 'statistic'.

Value

A list of 'data.frames' formatted for evaluation with 'sparrow::seas()'.

Examples

data(resultsDF)
ct.seasPrep(list('longer' = resultsDF, 'shorter' = resultsDF[1:10000,]), collapse.on = 'geneSymbol')

OscarBrock/gCrisprTools documentation built on Oct. 25, 2022, 7:29 a.m.