| Title: | Placental DNA methylation analysis tools |
|---|---|
| Description: | This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data. |
| Authors: | Victor Yuan [aut, cre], Wendy P. Robinson [ctb] |
| Maintainer: | Victor Yuan <[email protected]> |
| License: | GPL-2 |
| Version: | 1.13.0 |
| Built: | 2024-06-30 03:59:05 UTC |
| Source: | https://github.com/bioc/planet |
Coefficients from the three placental gestational age clocks from Lee Y et al. 2019.
Reference: Lee Y, Choufani S, Weksberg R, et al. Placental epigenetic clocks: estimating gestational age using placental DNA methylation levels. Aging (Albany NY). 2019;11(12):4238–4253. doi:10.18632/aging.102049. PMID: 31235674
data(ageCpGs)data(ageCpGs)
A tibble with coefficients for the RPC, CPC, and refined RPC.
1860 CpGs used to predict ethnicity.
See Yuan et al. 2019 for details.
data(ethnicityCpGs)data(ethnicityCpGs)
A character vector of length 1860
https://pubmed.ncbi.nlm.nih.gov/31399127/
These functions still work but will be removed (defunct) in the next version.
pl_infer_ethnicity: This function has been renamed
predictEthnicity
pl_infer_age: This function has been renamed
predictAge
6 DNA methylation profiles from preeclampsia and healthy control placentas. This data was downloaded from:
"Genome wide DNA methylation profiling of normal and preeclampsia placental samples. Illumina Infinium HumanMethylation450 BeadChip (450K array) was used to obtain DNA methylation profiles in placental samples. Samples included 16 samples from healthy uncomplicated pregnancies and 8 samples from pregnancies affected by preeclampsia." - from Yeung et al.
The DNA methylation data for 24 placental samples were downloaded from
GSE75196.
After normalizing using minfi::preprocessNoob and wateRmelon::BMIQ,
the data were filtered to 6/24 samples and 10,000 random CpGs + those CpGs
used in the gestational age clock and ethnicity classifier.
Reference: Yeung KR, Chiu CL, Pidsley R, Makris A et al. DNA methylation profiles in preeclampsia and healthy control placentas. Am J Physiol Heart Circ Physiol 2016 May 15;310(10):H1295-303. PMID:26968548
data(plBetas)data(plBetas)
A matrix
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75196
First trimester coefficients for placental cellular deconvolution from Yuan V et al. 2020.
Reference: to be edited PMID: to be edited
data(plCellCpGsFirst)data(plCellCpGsFirst)
A matrix with coefficients for Trophoblasts, Stromal, Endothelial, Hofbauer cells, nRBCs, and Syncytiotrophoblasts.
Third trimester coefficients for placental cellular deconvolution from Yuan V et al. 2020.
Reference: to be edited PMID: to be edited
data(plCellCpGsThird)data(plCellCpGsThird)
A matrix with coefficients for Trophoblasts, Stromal, Endothelial, Hofbauer cells, nRBCs, and Syncytiotrophoblasts.
A nice color palette for placental cell types.
Used in Yuan V et al. 2020.
Contains colors for:
Syncytiotrophoblast
Trophoblast
Stromal
Hofbauer
Endothelial
nRBCs
data(plColors)data(plColors)
An object of class character of length 6.
pl_betas
Sex, disease, and gestational age information associated with
pl_betas.
Downloaded from the GEO accession:
Reference: Yeung KR, Chiu CL, Pidsley R, Makris A et al. DNA methylation profiles in preeclampsia and healthy control placentas. Am J Physiol Heart Circ Physiol 2016 May 15;310(10):H1295-303. PMID: 26968548
data(plPhenoData)data(plPhenoData)
A tibble
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75196
predictAge Multiplies the coefficients from one of three
epigenetic gestational age clocks, by the corresponding CpGs in a supplied
betas data.frame.
predictAge(betas, type = "RPC")predictAge(betas, type = "RPC")
betas |
An n by m dataframe of methylation values on the beta scale (0, 1), where the CpGs are arranged in rows, and samples in columns. Should contain all CpGs used in each clock |
type |
One of the following: "RPC" (Robust), "CPC", (Control) or "RRPC" (Refined Robust). |
Predicts gestational age using one of 3 placental gestational age clocks: RPC, CPC, or refined RPC. Requires placental DNA methylation measured on the Infinium 27K/450k/EPIC methylation array. Ensure as many predictive CpGs are present in your data, otherwise accuracy may be impacted.
It's recommended that you have all predictive CpGs, otherwise accuracy may vary.
A vector of length m, containing inferred gestational age.
# Load placenta DNAm data library(dplyr) data(plBetas) data(plPhenoData) plPhenoData %>% mutate(inferred_ga = predictAge(plBetas, type = "RPC"))# Load placenta DNAm data library(dplyr) data(plBetas) data(plPhenoData) plPhenoData %>% mutate(inferred_ga = predictAge(plBetas, type = "RPC"))
Uses 1860 CpGs to predict self-reported ethnicity on placental microarray data.
predictEthnicity(betas, threshold = 0.75, force = FALSE)predictEthnicity(betas, threshold = 0.75, force = FALSE)
betas |
n x m dataframe of methylation values on the beta scale (0, 1), where the variables are arranged in rows, and samples in columns. Should contain all 1860 predictors and be normalized with NOOB and BMIQ. |
threshold |
A probability threshold ranging from (0, 1) to call samples 'ambiguous'. Defaults to 0.75. |
force |
run even if missing predictors. Default is |
Predicts self-reported ethnicity from 3 classes: Africans, Asians, and Caucasians, using placental DNA methylation data measured on the Infinium 450k/EPIC methylation array. Will return membership probabilities that often reflect genetic ancestry composition.
The input data should contain all 1860 predictors (cpgs) of the final GLMNET model.
It's recommended to use the same normalization methods used on the training data: NOOB and BMIQ.
a tibble
## To predict ethnicity on 450k/850k samples # Load placenta DNAm data data(plBetas) predictEthnicity(plBetas)## To predict ethnicity on 450k/850k samples # Load placenta DNAm data data(plBetas) predictEthnicity(plBetas)