getElementwiseStats: Find active elements by annotation

In klarman-cell-observatory/MAUDE: Mean Alterations Using Discrete Expression

Description

Tests guides for activity by considering a sliding window across the tested region and including all guides within the window for the test.

Usage

getElementwiseStats(experiments, normNBSummaries, elementIDs, tails = "both",
  nonTargeting = "NT", ...)

Arguments

experiments	a data.frame containing the headers that demarcate the screen ID, which are all also present in normNBSummaries
normNBSummaries	data.frame of guide-level statistics as generated by findGuideHits()
elementIDs	the names of one or more columns within guideLevelStats that contain the element annotations.
tails	whether to test for increased expression ("upper"), decreased ("lower"), or both ("both"); (defaults to "both")
nonTargeting	the name in normNBSummaries containing a logical representing whether or not the guide is non-Targeting (i.e. a negative control guide). Defaults to "NT"
...	other parameters for getZScalesWithNTGuides

Value

a data.frame containing the statistics for all elements

Examples

allGuideLevelStats = findGuideHitsAllScreens(myScreens, allDataCounts, allBinStats)
elementLevelStats = getElementwiseStats(unique(allGuideLevelStats["screen"]),allGuideLevelStats, elementIDs="element",tails="upper")

klarman-cell-observatory/MAUDE documentation built on Nov. 4, 2019, 3:53 p.m.