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epimedtools

Build Status Coverage Status

The epimedtools package provides set of useful statistical functions. This package rely on 'GEOquery' and 'affy' packages, R Reference Classes, caching features and memoisation to simplify, homogenize and speed up multi-omic analysis.

Data Structure

The epimedtools package aims to manage a study object composed of the three data structure: the data matrix and the two exp_grp and platform dataframes.

Take care:

  • study$data is a matrix of numerics
  • colnames(study$data) contains rownames(study$exp_grp)
  • rownames(study$data) contains rownames(study$platform)
> study
#' $data
#'       ctrl1 ctrl2 ctrl3 ctrl4 ctrl5 ctrl6 case1 case2 case3 case4 case5 case6
#' prb1  1.801 3.036 1.856 2.717 2.374 3.755 0.000 3.656 0.725 5.043 3.265 3.539
#' prb2  4.369 3.190 3.025 3.591 2.363 2.120 3.503 3.685 2.948 2.751 3.656 2.525
#' prb3  2.650 3.198 2.660 1.827 4.225 3.284 0.677 1.382 3.741 1.568 3.287 2.930
#' prb4  3.546 3.589 1.904 1.925 2.968 2.349 2.608 3.467 2.098 3.541 2.854 1.796
#' prb5  1.721 2.419 3.216 1.936 3.419 2.881 1.959 2.040 2.325 2.973 4.222 2.918
#' prb6  3.963 4.579 4.468 3.106 4.373 3.699 2.575 2.107 3.588 3.329 3.626 0.257
#' prb7  3.305 2.019 4.151 3.240 3.758 3.150 5.418 1.672 3.073 3.425 2.434 0.734
#' prb8  3.657 1.829 5.768 2.217 3.377 2.493 4.815 2.900 4.521 4.502 2.144 3.973
#' prb9  2.158 3.413 3.564 2.754 2.634 2.556 2.868 1.514 2.705 4.202 2.030 1.197
#' prb10 3.390 2.958 2.204 4.523 2.152 4.561 1.629 0.891 2.519 2.783 1.541 2.375
#'
#' $exp_grp
#'          sex age      tabac treatment histo
#' ctrl1 Female  23     Smoker      0 ug  lung
#' ctrl2   Male  28     Smoker      0 ug  lung
#' ctrl3 Female  26     Smoker      0 ug  lung
#' ctrl4 Female  30 Non Smoker      0 ug  lung
#' ctrl5   Male  22 Non Smoker      0 ug  lung
#' ctrl6   Male  23 Non Smoker      0 ug  lung
#' case1   Male  25     Smoker     15 ug  lung
#' case2 Female  27     Smoker     15 ug  lung
#' case3   Male  29     Smoker     15 ug  lung
#' case4 Female  23 Non Smoker     15 ug  lung
#' case5   Male  23 Non Smoker     15 ug  lung
#' case6   Male  25 Non Smoker     15 ug  lung
#'
#' $platform
#'         GB_ACC      Species Gene Symbol ENTREZ_GENE_ID
#' prb1   1U48705 Homo sapiens        DDR1            780
#' prb2   2M87338 Homo sapiens        RFC2           5982
#' prb3   3X51757 Homo sapiens       HSPA6           3310
#' prb4   4X69699 Homo sapiens        PAX8           7849
#' prb5   5L36861 Homo sapiens      GUCA1A           2978
#' prb6   6L13852 Homo sapiens        UBA7           7318
#' prb7   7X55005 Homo sapiens        THRA           7067
#' prb8   8X79510 Homo sapiens      PTPN21          11099
#' prb9   9M21121 Homo sapiens        CCL5           6352
#' prb10  1J02843 Homo sapiens      CYP2E1           1571

Treatment and Analysis Features

The epimedtools package provides not only a set of treatment features like data fetching or normalization, but also genome and genes anlysis tools.

Installation

To get the current development version from github, you need first to install following packages from bioconductor:

  • Biobase
  • affy
  • GEOquery
# install.packages("BiocManager")
BiocManager::install(c("Biobase", "affy", "GEOquery"))

Then, install epimedtool:

# install.packages("devtools")
devtools::install_github("fchuffar/epimedtools")

Vignettes

To browse available vignettes:

browseVignettes(package = 'epimedtools')