Description Objects from the Class Slots Extends Methods Note Author(s) See Also Examples
This class is defined to summarize the enrichment analysis about a chromosome.
chromosome
is defined to build an object of class
Chromosome
in order to compute an enrichment analysis.
A Chromosome
object contains the original data,
a list of SNPs, some results and resampling data.
When created, an Chromosome
object is "empty".
readEnrichment
initializes a Chromosome
object with value from PLINK computation and user's files.
In this step, only the fields "Data", "LD", "SNP" are filled.
reSample
fills the fields: Table, EnrichmentRatio, Z, PValue and Resampling of a Chromosome
.
Note that if reSample
is executed on an Chromosome
every new resampling
is added to the original ones, pre-existing statistics are erased and computed again with the new resampling set.
[data.frame]: a data.frame
with 6 columns ("SNP", "PVALUE", "CHR", "MAF", "eSNP", "xSNP"). Where "eSNP" and "xSNP" are logical columns defining the lists of SNPs (extended or not).
[data.frame]: a data.frame
which contains LD informations between SNPs (computed with writeLD
or PLINK).
[SNP]: contain a EnrichSNP
object (whith slots: SNP, Table, EnrichmentRatio, Z, PValue and Resampling) for a list of SNPs (eSNP
) and an extended one (xSNP
).
Class EnrichSNP
, directly.
Generate and initialize a new Chromosome
object.
Get the value of the field slotName
.
Set value
to the field slotName
.
Return the formatted values of Chromosome
object.
Chromosome
object is not intended to be used alone on this version.\
It is a part of the Enrichment
object.
Mickael Canouil mickael.canouil@good.ibl.fr
Overview : snpEnrichment-package
Classes : Enrichment
, Chromosome
, EnrichSNP
Methods : plot
, reSample
, getEnrichSNP
, excludeSNP
, compareEnrichment
,
enrichment
, is.enrichment
, chromosome
, is.chromosome
Functions : initFiles
, writeLD
, readEnrichment
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | Data <- structure(
list(
SNP = c("rs4970420", "rs3766178",
"rs10910030", "rs10910036",
"rs2234167", "rs6661861"),
PVALUE = c(0.9244, 0.167, 0.01177, 0.4267, 0.9728, 0.4063),
CHR = c(1, 1, 1, 1, 1, 1),
POS = c(1106473, 1478180, 2035684, 2183754, 2494330, 3043121),
MAF = c(0.2149, 0.3117, 0.374, 0.3753, 0.1565, 0.06101),
eSNP = c(0, 1, 1, 0, 0, 0),
xSNP = c(0, 1, 1, 0, 0, 0)
),
.Names = c("SNP", "PVALUE", "CHR", "POS", "MAF", "eSNP", "xSNP"),
row.names = c("rs4970420", "rs3766178",
"rs10910030", "rs10910036",
"rs2234167", "rs6661861"),
class = "data.frame")
toyChr <- chromosome(Data = Data)
show(toyChr)
toyChr
toyChr <- chromosome()
toyChr["Data"] <- Data
toyChr
is.chromosome(toyChr) # TRUE
|
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