Build AMR vector — AMR_build • hdmax2

Build AMR from the result of function AMR_search

Usage

AMR_build(res, methylation, nb_cpg = 2)

Arguments

res: result object of function AMR_search
methylation: a matrix of methylation profile.
nb_cpg: threshold of minimal number of CpG in the AMR

Value

A set of build AMRs.

res, selected AMR
CpG_for_each_AMR, list of markers present on each AMR.
AMR_acp, first components of PCA for each DMR
AMR_mean, mean value of CpG on the AMR

Details

We use the series of pValues (one pValue per CpGs) obtained with the mEWAS regression method and the combination of pValue max2. To determine the potential AMRs used the combp method present in the ENmix package (Xu et al. 2016). This method uses the Fisher method to combine the pValues and also the base pair distance (bP) between CpGs (1000 bP maximum between nb_cpg CpGs on the same AMR). The information for each AMR is summarized by doing the mean (by row) of each CpG.

Author

Basile Jumentier

Examples

data = hdmax2::helper_ex
K=5
## run hdmax2 step1
hdmax2_step1 = hdmax2::run_AS(exposure = data$exposure,
                             outcome = data$phenotype,
                             M = data$methylation,
                             K = K)
#> Running first regression with univariate exposure variable.
#> Running second regression.
#> Running max-squared test.

##Detecting AMR
chr = data$annotation$chr
start = data$annotation$start
end = data$annotation$end
pval = hdmax2_step1$max2_pvalues
cpg = data$annotation$cpg

res.amr_search = hdmax2::AMR_search(
chr = data$annotation$chr,
start = data$annotation$start,
end = data$annotation$end,
pval = hdmax2_step1$max2_pvalues,
cpg = data$annotation$cpg,
seed = 0.7, #Careful to change this parameter when working with real data
nCores = 2)

res.amr_search$res
#>   chr  start    end          p        fdr
#> 3   1 864893 865027 0.03604853 0.05184658
#> 2   1 858380 858381 0.03901609 0.05184658
#> 4   1 886431 886553 0.04077365 0.05184658
#> 5   1 896773 896774 0.05000351 0.05184658
#> 1   1 854778 855056 0.05184658 0.05184658

res.arm_build = hdmax2::AMR_build(res.amr_search, 
methylation = data$methylation, nb_cpg = 2)
#List of DMR selected
head(res.arm_build$res)
#>    DMR chr  start    end          p        fdr nb
#> 1 DMR1   1 886431 886553 0.04077365 0.05184658  3
#> 2 DMR2   1 854778 855056 0.05184658 0.05184658  6
## CpG in the DMR
res.arm_build$CpG_for_each_AMR
#> $DMR1
#> [1] "cg20322444" "cg07983659" "cg11733071"
#> 
#> $DMR2
#> [1] "cg08029603" "cg16347928" "cg22699361" "cg03890988" "cg21786289"
#> [6] "cg13897241"
#>