mergeResults {derfinder} | R Documentation

## Merge results from different chromosomes

### Description

This function merges the results from running analyzeChr on several chromosomes and assigns genomic states using annotateRegions. It re-calculates the p-values and q-values using the pooled areas from the null regions from all chromosomes. Once the results have been merged, `derfinderReport::generateReport` can be used to generate an HTML report of the results. The `derfinderReport` package is available at https://github.com/lcolladotor/derfinderReport.

### Usage

    mergeResults(chrs = c(1:22, "X", "Y"), prefix = ".",
      significantCut = c(0.05, 0.1), genomicState, minoverlap = 20,
      mergePrep = FALSE, ...)

### Arguments

`chrs` | The chromosomes of the files to be merged.
`prefix` | The main data directory path, which can be useful if analyzeChr is used for several parameters and the results are saved in different directories.
`significantCut` | A vector of length two specifiying the cutoffs used to determine significance. The first element is used to determine significance for the P-values and FWER adjusted P-values, while the second element is used for the Q-values (FDR adjusted P-values) similar to calculatePvalues.
`genomicState` | A GRanges object created with makeGenomicState. It can be either the `genomicState$fullGenome` or `genomicState$codingGenome` component.
`minoverlap` | Determines the mininum overlap needed when annotating regions with annotateRegions.
`mergePrep` | If `TRUE` the output from preprocessCoverage is merged.
`...` | Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If `TRUE` basic status updates will be printed along the way. optionsStats The options used in analyzeChr. By default `NULL` and will be inferred from the output files. cutoffFstatUsed The actual F-statistic cutoff used. This can be obtained from the logs or from the output of analyzeChr. If `NULL` then this function will attempt to re-calculate it. Passed to annotateRegions and extendedMapSeqlevels.

### Details

If you want to calculate the FWER adjusted P-values, supply `optionsStats` which is produced by analyzeChr.

### Value

Seven Rdata files.

fullFstats.Rdata

  Full F-statistics from all chromosomes in a list of Rle objects.

fullTime.Rdata

  Timing information from all chromosomes.

fullNullSummary.Rdata

  A DataFrame with the null region information: statistic, width, chromosome and permutation identifier. It's ordered by the statistics

fullRegions.Rdata

  GRanges object with regions found and with full annotation from matchGenes. Note that the column `strand` from matchGenes is renamed to `annoStrand` to comply with GRanges specifications.

fullCoveragePrep.Rdata

  A list with the pre-processed coverage data from all chromosomes.

fullAnnotatedRegions.Rdata

  A list as constructed in annotateRegions with the assigned genomic states.

optionsMerge.Rdata

  A list with the options used when merging the results. Used in `derfinderReport::generateReport`.

### Author(s)

Leonardo Collado-Torres

### See Also

analyzeChr, calculatePvalues, annotateRegions

### Examples

    ## The output will be saved in the 'generateReport-example' directory
    dir.create('generateReport-example', showWarnings = FALSE, recursive = TRUE)

    ## For convenience, the derfinder output has been pre-computed
    file.copy(system.file(file.path('extdata', 'chr21'), package='derfinder',
    mustWork=TRUE), 'generateReport-example', recursive=TRUE)

    ## Merge the results from the different chromosomes. In this case, there's
    ## only one: chr21
    mergeResults(chrs='21', prefix='generateReport-example',
    genomicState=genomicState$fullGenome)

    ## Not run:
    ## You can then explore the wallclock time spent on each step
    load(file.path('generateReport-example', 'fullRegions.Rdata'))

    ## Process the time info
    time <- lapply(fullTime, function(x) data.frame(diff(x)))
    time <- do.call(rbind, time)
    colnames(time) <- 'sec'
    time$sec <- as.integer(round(time$sec))
    time$min <- time$sec / 60
    time$chr <- paste0('chr', gsub('\\..*', '', rownames(time)))
    time$step <- gsub('.*\\.', '', rownames(time))
    rownames(time) <- seq_len(nrow(time))

    ## Make plot
    library('ggplot2')
    ggplot(time, aes(x=step, y=min, colour=chr)) + geom_point() +
        labs(title='Wallclock time by step') +
        scale_colour_discrete(limits=chrs) +
        scale_x_discrete(limits=names(fullTime[[1]])[-1]) + ylab('Time (min)') +
        xlab('Step')

    ## End(Not run)

[Package derfinder version 1.20.0 Index]