An S4 class Enrichment

This class is defined to summarize the enrichment analysis on each chromosomes and the whole genome.

Slots

Signal

A three columns data.frame: "SNP", "PVALUE" and "IN" (e.g., GWAS). "IN" is computed during the reading step and gives informations about which SNPs are kept for the enrichment analysis.

Loss

A four columns data.frame: "Rows", "Unique", "Intersect.Ref.Signal" and "CIS". This slot gives information on data losses.

Call

Each parameters used for the reading or resampling step are stored in this slot.

eSNP

Contain a EnrichSNP object for a list of SNPs (eSNP).

xSNP

Contain a EnrichSNP object for a extended list of SNPs (xSNP).

Chromosomes

A list of 22 Chromosome objects.

Objects from the Class

Enrichment is defined to build an object of class Enrichment in order to compute an enrichment analysis. Enrichment is the object containing the results for all Chromosome object and for the whole genome.

When an Enrichment object is created, it contains a list of SNPs (e.g., eSNPs). All the others slots are "empty". After reSample is ran on an Enrichment object, the slots: Table, EnrichmentRatio, Z, PValue and Resampling are filled.

Note that if reSample is executed on an Enrichment every new resampling is added to the original ones, pre-existing statistics are erased and computed again with the new resampling set.

Examples

data(toyEnrichment)
toyEnrich <- enrichment()
show(toyEnrich)
#>     ~~~ Class: Enrichment ~~~ 
#>  ~ Loss : (0x0) NA
#>  ~ Call :
#>     readEnrichment() : Not yet called.    reSample() : Not yet called.
#>  ~ eSNP :
#>    - List : (0) NA
#>    - Table : (2x2) NA
#>    - EnrichmentRatio : NA
#>    - Z               : NA
#>    - PValue          : NA
#>    - Resampling      : (0x5) 0
#> 
#>  ~ xSNP :
#>    - List : (0) NA
#>    - Table : (2x2) NA
#>    - EnrichmentRatio : NA
#>    - Z               : NA
#>    - PValue          : NA
#>    - Resampling      : (0x5) 0
#> 
#>  ~ Chromosomes : 22/22 empty Chromosomes

toyEnrich["Loss"] <- toyEnrichment["Loss"]
toyEnrich["Loss"]
#>          Rows Unique Intersect.Signal  CIS
#> Signal  10000  10000             9978 9978
#> Genome   1333   1333             1330 1330
#> Chrom1    104    104              104  104
#> Chrom2    110    110              110  110
#> Chrom3     95     95               95   95
#> Chrom4     83     83               83   83
#> Chrom5     94     94               94   94
#> Chrom6     91     91               91   91
#> Chrom7     78     78               78   78
#> Chrom8     86     86               86   86
#> Chrom9     66     66               66   66
#> Chrom10    62     62               62   62
#> Chrom11    81     81               81   81
#> Chrom12    62     62               61   61
#> Chrom13    48     48               48   48
#> Chrom14    34     34               34   34
#> Chrom15    37     37               36   36
#> Chrom16    37     37               37   37
#> Chrom17    34     34               34   34
#> Chrom18    34     34               34   34
#> Chrom19    26     26               26   26
#> Chrom20    30     30               30   30
#> Chrom21    18     18               17   17
#> Chrom22    23     23               23   23

toyEnrich <- enrichment(Loss = toyEnrichment["Loss"], eSNP = toyEnrichment["eSNP"])
toyEnrich <- enrichment(Loss = toyEnrichment["Loss"])

if (interactive()) {
  reSample(
    object = toyEnrichment,
    nSample = 10,
    empiricPvalue = TRUE,
    MAFpool = c(0.05, 0.10, 0.2, 0.3, 0.4, 0.5),
    mc.cores = 1,
    onlyGenome = TRUE
  )
  print(toyEnrichment)

  excludeFile <- c(
    "rs7897180", "rs4725479", "rs315404", "rs17390391", "rs1650670",
    "rs6783390", "rs1642009", "rs4756586", "rs11995037", "rs4977345",
    "rs13136448", "rs4233536", "rs11151079", "rs2299657", "rs4833930",
    "rs1384", "rs7168184", "rs6909895", "rs7972667", "rs2293229",
    "rs918216", "rs6040608", "rs2817715", "rs13233541", "rs4486743",
    "rs2127806", "rs10912854", "rs1869052", "rs9853549", "rs448658",
    "rs2451583", "rs17483288", "rs10962314", "rs9612059", "rs1384182",
    "rs8049208", "rs12215176", "rs2980996", "rs1736976", "rs8089268",
    "rs10832329", "rs12446540", "rs7676237", "rs869922", "rs16823426",
    "rs1374393", "rs13268781", "rs11134505", "rs7325241", "rs7520109"
  )

  toyEnrichment_exclude <- excludeSNP(toyEnrichment, excludeFile, mc.cores = 1)
  print(toyEnrichment_exclude)
}