meaRtools: permute_features_and_plot – R documentation

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permute_features_and_plot

Write PDF

Description

Generates a PDF containing plots and p-values for each feature. P-values are generating using Mann Whitney and permutation tests. This function requires that you create a list of dataframes for a given feature type (e.g. spikes) using the aggregate.data() function

Usage

permute_features_and_plot(s, wt, np, features_list, type, output_dir)

Arguments

`s`	MEA data structure
`wt`	The treatment that will act as the wildtype/reference for the Mann Whitney and Permutation tests
`np`	Number of permutations to be performed
`features_list`	A list of dataframes containing data for a given feature
`type`	Type of features contained in features_list (e.g. spikes, ns, or bursts)
`output_dir`	Directory where output files will be generated

Value

A PDF file containing the plots and p-values.

Author(s)

Ryan Dhindsa

Examples

data("S")
	spike_features<-aggregate_features(S, feat_type="spike" )
	wt <- "untreated"
	output_dir = tempdir()
  print(paste0("Creating output folders under ",output_dir))
	permute_features_and_plot(S, wt, np, spike_features, "spikes", output_dir)

meaRtools

Micro-Electro Array (MEA) Analysis

v1.0.4

GPL (>= 3)

Authors

Quanli Wang [aut, ctb], Sahar Gelfman [aut, ctb, cre], Diana Hall [aut, ctb], Ryan Dhindsa [aut, ctb], Matt Halvorsen [aut, ctb], Ellese Cotterill [aut, ctb], Tom Edinburgh [aut, ctb], Stephen J. Eglen [aut, ctb, ths]

Initial release

2018-7-1