Description Usage Arguments Value Author(s) Examples
View source: R/methylInheritanceInternalMethods.R
Run CpG site or region analysis using the methylKit
package for each generation present in the dataset. The intersection of
conserved elements is obtained for each group of two consecutive
generations, as well as, for larger group subset. The output of the
analysis is saved in a RDS file when an directory is
specified.
1 2 3 4 5 6  runOnePermutationOnAllGenerations(id, methylInfoForAllGenerations,
type = c("both", "sites", "tiles"), outputDir = NULL,
nbrCoresDiffMeth = 1, minReads = 10, minMethDiff = 10,
qvalue = 0.01, maxPercReads = 99.9, destrand = FALSE,
minCovBasesForTiles = 0, tileSize = 1000, stepSize = 1000,
restartCalculation, saveInfoByGeneration)

id 
an 
methylInfoForAllGenerations 
a 
type 
One of the "sites","tiles" or "both" strings. Specifies the type of differentially methylated elements should be returned. For retrieving differentially methylated bases type="sites"; for differentially methylated regions type="tiles". Default: "both". 
outputDir 
a string, the name of the directory that will contain the results of the permutation. If the directory does not exist, it will be created. 
nbrCoresDiffMeth 
a positive integer, the number of cores to use for
parallel differential methylation calculations.Parameter used for both
sites and tiles analysis. The parameter
corresponds to the 
minReads 
a positive 
minMethDiff 
a positive integer betwwen [0,100], the absolute value
of methylation percentage change between cases and controls. The parameter
correspond to the 
qvalue 
a positive 
maxPercReads 
a double between [0100], the percentile of read
counts that is going to be used as upper cutoff. Bases ore regions
having higher
coverage than this percentile are discarded. Parameter used for both CpG
sites and tiles analysis. The parameter
correspond to the 
destrand 
a logical, when 
minCovBasesForTiles 
a nonnegative integer, the minimum number of
bases to be covered in a given tiling window. The parameter
corresponds to the 
tileSize 
a positive integer, the size of the tiling window. The
parameter corresponds to the 
stepSize 
a positive integer, the step size of tiling windows. The
parameter corresponds to the 
restartCalculation 
a 
saveInfoByGeneration 
a 
a list
containing the following elements:
SITES
Only present when type
= "sites"
or
"both"
, a list
containing:
i2
a list
containing:
HYPER
a list
of integer
, the number of conserved
hyper differentially methylated sites between two consecutive generations.
The first element represents the intersection of the first and second
generations; the second element, the intersection of the second and third
generations; etc..
HYPO
a list
of integer
, the number of conserved
hypo differentially methylated sites between two consecutive generations.The
first element represents the intersection of the first and second
generations; the second element, the intersection of the second and third
generations; etc..
iAll
a list
containing:
HYPER
a list
of integer
, the number of conserved
hyper differentially methylated sites between three or more consecutive
generations. The first element represents the intersection of the first
three generations; the second element, the intersection of the first fourth
generations; etc..The number of entries depends of the number
of generations.
HYPO
a list
of integer
, the number of conserved
hypo differentially methylated sites between three or more consecutive
generations. The first element represents the intersection of the first
three generations; the second element, the intersection of the first fourth
generations; etc..The number of entries depends of the number of
generations.
TILES
Only present when type
= "tiles"
or
"both"
, a list
containing:
itemize
i2
a list
containing:
HYPER
a list
of integer
, the number of conserved
hyper differentially methylated positions between two consecutive
generations. The first element represents the intersection of the
first and second generations; the second element, the intersection of
the second and third generations; etc..
HYPO
a list
of integer
, the number of conserved
hypo differentially methylated positions between two consecutive
generations.The first element represents the intersection of the first and
second generations; the second element, the intersection of the second
and third generations; etc..
iAll
a list
containing:
HYPER
a list
of integer
, the number of conserved
hyper differentially methylated positions between three or more consecutive
generations. The first element represents the intersection of the first
three generations; the second element, the intersection of the first fourth
generations; etc..The number of entries depends of the number
of generations.
HYPO
a list
of integer
, the number of conserved
hypo differentially methylated positions between three or more consecutive
generations. The first element represents the intersection of the first
three generations; the second element, the intersection of the first fourth
generations; etc..The number of entries depends of the number of
generations.
Astrid Deschenes, Pascal Belleau
1 2 3 4 5 6 7 8 9 10  ## Load methyl information
data(samplesForTransgenerationalAnalysis)
## Run a permutation analysis
methylInheritance:::runOnePermutationOnAllGenerations(id = 2,
methylInfoForAllGenerations = samplesForTransgenerationalAnalysis,
type = "tiles", outputDir = NULL,
nbrCoresDiffMeth = 1, minReads = 10, minMethDiff = 10, qvalue = 0.01,
maxPercReads = 99.9, destrand = FALSE, minCovBasesForTiles = 0,
tileSize = 1000, stepSize = 1000, restartCalculation = FALSE)

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