ct.seasPrep {gCrisprTools} | R Documentation

## 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')

[Package gCrisprTools version 2.0.0 Index]