Description Usage Arguments Value Author(s) See Also Examples
Calls cpg.assoc
to get the observed P-values from the study and then performs a user-specified number of permutations to calculate an emperical p-value.
In addition to the same test statistics computed by cpg.assoc
, cpg.perm
will compute the permutation p-values for the observed p-value, the number of Holm significant sites, and the number of FDR significant sites.
1 2 3 |
beta.values |
A vector, matrix, or data frame containing the beta values of interest (1 row per CpG site, 1 column per individual). |
indep |
A vector containing the main variable of interest. |
covariates |
A data frame consisting of the covariates of interest. covariates can also be a matrix if it is a model matrix minus the intercept column.
It can also be a vector if there is only one covariate of interest. Can also be a formula(e.g. |
nperm |
The number of permutations to be performed. |
data |
an optional data frame, list or environment (or object coercible by |
seed |
The required seed for random number generation. If not input, will use R's internal seed. |
logit.transform |
logical. If |
chip.id |
An optional vector containing chip, batch identities, or other categorical factor of interest to the researcher. If specified, chip id will be included as a factor in the model. |
subset |
An optional logical vector specifying a subset of observations to be used in the fitting process. |
random |
logical. If |
fdr.cutoff |
The threshold at which to compare the FDR values. The default setting is .05. Any FDR values less than .05 will be considered significant. |
fdr.method |
Character. Method used to calculate False Discovery Rate. Can be any of the methods listed in |
large.data |
Logical. Enables analyses of large datasets. When |
The item returned will be of class "cpg.perm"
. It will contain all of the values of class cpg (cpg.assoc
) and a few more:
permutation.matrix |
A matrix consisting of the minimum observed P-value, the number of Holm significant CpG sites, and the number of FDR significant sites for each permutation. |
gc.permutation.matrix |
Similar to the permutation.matrix only in relation to the genomic control adjusted p-values. |
perm.p.values |
A data frame consisting of the permutation P-values, and the number of permutations performed. |
perm.tstat |
If one hundred or more permutations were performed and indep is a continuous variable, consists of the quantile .025 and .975 of observed t-statistcs for each permutation, ordered from smallest to largest.
perm.tstat is used by |
perm.pval |
If one hundred or more permutations were performed, consists of the observed p-values for each permutation, ordered from smallest to largest. perm.pval is usd by |
Barfield, R.; Conneely, K.; Kilaru,V.
Maintainer: R. Barfield: <rbarfield01@fas.harvard.edu>
cpg.assoc
cpg.work
plot.cpg
scatterplot
cpg.combine
manhattan
plot.cpg.perm
sort.cpg.perm
sort.cpg
cpg.qc
1 2 3 4 5 6 7 8 9 10 11 12 | ##Loading the data
data(samplecpg,samplepheno,package="CpGassoc")
###NOTE: If you are dealing with large data, do not specify large.data=FALSE.
###The default option is true.
##This will involve partitioning up the data and performing more gc() to clear up space
#Performing a permutation 10 times
Testperm<-cpg.perm(samplecpg[1:200,],samplepheno$weight,seed=2314,nperm=10,large.data=FALSE)
Testperm
#All the contents of CpGassoc are included in the output from Testperm
#summary function works on objects of class cpg.perm
summary(Testperm)
|
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