added new Wu clock

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: methylclock
 Type: Package
 Title: Chronological and gestational DNAm age estimation using different methylation-based clocks
-Version: 0.7.0
-Date: 2021-03-24
+Version: 0.7.2
+Date: 2021-04-26
 Authors@R: c( person("Dolors", "Pelegri-Siso", , "[email protected]", role = "aut"),
               person("Juan R.", "Gonzalez", ,"[email protected]", role = c("aut", "cre")))
 Description: Package to estimate DNA methylation age (DNAmAge) using different methylation clocks. 

R/DNAmGA.R

@@ -68,7 +68,8 @@ DNAmGA <- function(x, toBetas = FALSE,
     as.character(coefKnightGA$CpGmarker[-1]),
     coefBohlin$CpGmarker[-1],
     as.character(coefMayneGA$CpGmarker[-1]),
-    as.character(coefLeeGA$CpGmarker[-1])
+    as.character(coefLeeGA$CpGmarker[-1]),
+    as.character(coefWuGA$CpGmarker[-1])
   )
 
   if (any(!cpgs.all %in% colnames(cpgs))) {
@@ -134,6 +135,16 @@ DNAmGA <- function(x, toBetas = FALSE,
     Mayne = mayne
   )
 
+
+  # --------------> Wu
+
+  wu <- predAge(cpgs.imp, coefWuGA, intercept = TRUE)
+  Wu <- data.frame(
+    id = rownames(cpgs.imp),
+    Wu = wu
+  )
+
+
   # --------------> Lee
 
 
@@ -186,6 +197,7 @@ DNAmGA <- function(x, toBetas = FALSE,
       Knight <- ageAcc1(Knight, age, lab = "Knight")
       Bohlin <- ageAcc1(Bohlin, age, lab = "Bohlin")
       Mayne <- ageAcc1(Mayne, age, lab = "Mayne")
+      Wu <- ageAcc1(Wu, age, lab = "Wu")
     }
     else {
       cell.counts <- try(meffil.estimate.cell.counts.from.betas(
@@ -202,6 +214,7 @@ DNAmGA <- function(x, toBetas = FALSE,
         Knight <- ageAcc2(Knight, df, lab = "Knight")
         Bohlin <- ageAcc2(Bohlin, df, lab = "Bohlin")
         Mayne <- ageAcc2(Mayne, df, lab = "Mayne")
+        Wu <- ageAcc2(Wu, df, lab = "Wu")
       }
     }
   }
@@ -212,6 +225,7 @@ DNAmGA <- function(x, toBetas = FALSE,
   out <- Knight %>%
     full_join(Bohlin, by = "id") %>%
     full_join(Mayne, by = "id") %>%
+    full_join(Wu, by = "id") %>%
     full_join(Lee, by = "id")
   out <- tibble::as_tibble(out)
 

R/checkClocksGA.R

@@ -27,21 +27,24 @@ checkClocksGA <- function(x, ...) {
   coefBoh <- coefBohlin$CpGmarker[-1][!coefBohlin$CpGmarker[-1] %in% cpg.names]
   checkBohlin <- coefBoh[!coefBoh %in% cpg.names]
   checkMayne <- coefMayneGA$CpGmarker[-1][!coefMayneGA$CpGmarker[-1] %in% cpg.names]
+  checkWu <- coefWuGA$CpGmarker[-1][!coefWuGA$CpGmarker[-1] %in% cpg.names]
   checkLee <- coefLeeGA$CpGmarker[-1][!coefLeeGA$CpGmarker[-1] %in% cpg.names]
 
 
   sizes <- c(
     length(checkKnight), length(checkBohlin),
-    length(checkMayne), length(checkLee)
+    length(checkMayne), length(checkWu), 
+    length(checkLee)
   )
 
   n <- c(
     nrow(coefKnightGA) - 1, length(coefBoh),
-    nrow(coefMayneGA) - 1, nrow(coefLeeGA) - 1
+    nrow(coefMayneGA) - 1, nrow(coefWuGA) - 1.
+    nrow(coefLeeGA) - 1
   )
 
   df <- data.frame(
-    clock = c("Knight", "Bohlin", "Mayne", "Lee"),
+    clock = c("Knight", "Bohlin", "Mayne", "Wu", "Lee"),
     Cpgs_in_clock = n,
     missing_CpGs = sizes,
     percentage = round((sizes / n) * 100, 1)
@@ -54,7 +57,7 @@ checkClocksGA <- function(x, ...) {
 
     out <- list(
       Knight = checkKnight, Bohlin = checkBohlin,
-      Mayne = checkMayne, Lee = checkLee
+      Mayne = checkMayne, Wu = checkWy, Lee = checkLee
     )
   }
   else {

vignettes/methylclock.Rmd

@@ -47,6 +47,7 @@ This manual describes how to estimate chronological and gestational DNA methylat
 - **Knight's clock**: It uses 148 CpGs described in @knight2016epigenetic. It was trained using 27K and 450K arrays in cord blood samples.
 - **Bohlin's clock**: It uses 96 CpGs described in @bohlin2016prediction. It was trained using 450K array in cord blood samples.
 - **Mayne's clock**: It uses 62 CpGs described in @mayne2017accelerated. It was trained using 27K and 450K.
+- **Wu's clock**: It uses 111 CpGs described in @wu2019dna. It was trained using 27K and 450K.
 - **Lee's clocks**: Three different biological clocks described in @lee2019placental are implemented. It was trained for 450K and EPIC arrays in placenta samples.
      - **RPC clock**: Robust placental clock (RPC). It uses 558 CpG sites.
      - **CPC clock**: Control placental clock (CPC). It usses 546 CpG sites.

vignettes/methylclock.bib

@@ -1,3 +1,14 @@
+@article{wu2019dna,
+  title={DNA methylation profile is a quantitative measure of biological aging in children},
+  author={Wu, Xiaohui and Chen, Weidan and Lin, Fangqin and Huang, Qingsheng and Zhong, Jiayong and Gao, Huan and Song, Yanyan and Liang, Huiying},
+  journal={Aging (Albany NY)},
+  volume={11},
+  number={22},
+  pages={10031},
+  year={2019},
+  publisher={Impact Journals, LLC}
+}
+
 @article{mcewen2019pedbe,
   title={The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells},
   author={McEwen, Lisa M and O?Donnell, Kieran J and McGill, Megan G and Edgar, Rachel D and Jones, Meaghan J and MacIsaac, Julia L and Lin, David Tse Shen and Ramadori, Katia and Morin, Alexander and Gladish, Nicole and others},