evalDetection: Evaluate detection performance of a signal detector

Description Usage Arguments Details Value Examples

View source: R/evalDetection.R

Description

For a given cutpoint (e.g., previously estimated with the function estimateCutPoint), 'evalDetection' will return the evaluation of the methylation signal into two clases: signal from control and signal from treatment samples.

Usage

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evalDetection(LR, control.names, treatment.names, cutpoint, div.col = 7L,
  seed = 1234, verbose = TRUE)

Arguments

LR

A list of GRanges objects (LR) including control and treatment GRanges containing divergence values for each cytosine site in the meta-column. LR can be generated, for example, by the function estimateDivergence. Each GRanges object must correspond to a sample. For example, if a sample is named 's1', then this sample can be accessed in the list of GRanges objects as LR$s1.

control.names

Names/IDs of the control samples, which must be include in the variable LR.

treatment.names

Names/IDs of the treatment samples, which must be included in the variable LR.

cutpoint

Cutpoint to select DIMPs. Cytosine positions with divergence greater than 'cutpoint' will selected as DIMPs. Cutpoints are estimated with the function 'estimateCutPoint'. Cytosine positions with divergence values greater than the cutpoint are considered members of the "positive class".

div.col

Column number for divergence variable used in the ROC analysis and estimation of the cutpoints.

seed

Random seed used for random number generation.

verbose

if TRUE, prints the function log to stdout

Details

The regulatory methylation signal is also an output from a natural process that continuously takes place across the ontogenetic development of the organisms. So, we expect to see methylation signal under natural, ordinary conditions. Here, to evaluate the performance of signal classification obtained with the application of some classifier/detector or rule, the cross-tabulation of observed and predicted classes with associated statistics are calculated with function confusionMatrix fron package "caret".

A classification result with low accuracy and compromising values from other classification performance indicators (see below) suggest that the treatment does not induce a significant regulatory signal different from control.

Value

the list with the statisitics returned by the function confusionMatrix fron package "caret".

Examples

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set.seed(123) #'#' To set a seed for random number generation
#'#' GRanges object of the reference with methylation levels in
#'#' its matacolumn
num.points <- 5000
Ref <- makeGRangesFromDataFrame(
  data.frame(chr = '1',
             start = 1:num.points,
             end = 1:num.points,
             strand = '*',
             p1 = rbeta(num.points, shape1 = 1, shape2 = 1.5)),
  keep.extra.columns = TRUE)

#'#' List of Granges objects of individuals methylation levels
Indiv <- GRangesList(
  sample11 = makeGRangesFromDataFrame(
    data.frame(chr = '1',
               start = 1:num.points,
               end = 1:num.points,
               strand = '*',
               p2 = rbeta(num.points, shape1 = 1.5, shape2 = 2)),
    keep.extra.columns = TRUE),
  sample12 = makeGRangesFromDataFrame(
    data.frame(chr = '1',
               start = 1:num.points,
               end = 1:num.points,
               strand = '*',
               p2 = rbeta(num.points, shape1 = 1.6, shape2 = 2)),
    keep.extra.columns = TRUE),
  sample21 = makeGRangesFromDataFrame(
    data.frame(chr = '1',
               start = 1:num.points,
               end = 1:num.points,
               strand = '*',
               p2 = rbeta(num.points, shape1 = 40, shape2 = 4)),
    keep.extra.columns = TRUE),
  sample22 = makeGRangesFromDataFrame(
    data.frame(chr = '1',
               start = 1:num.points,
               end = 1:num.points,
               strand = '*',
               p2 = rbeta(num.points, shape1 = 41, shape2 = 4)),
    keep.extra.columns = TRUE))
#'#' To estimate Hellinger divergence using only the methylation levels.
HD <- estimateDivergence(ref = Ref, indiv = Indiv, meth.level = TRUE,
                         columns = 1)
res <- evalDetection(LR  = HD, control.names = c("sample11", "sample12"),
                     treatment.names = c("sample21", "sample22"),
                     cutpoint = 0.85, div.col = 3L, seed=1234, verbose=TRUE)

genomaths/MethylIT.utils documentation built on Nov. 26, 2019, 2:10 a.m.