sequencing.annotate: Annotate a bisulfite sequencing experiment (WGBS or RRBS)...

In timpeters82/DMRcate-devel: Methylation array and sequencing spatial analysis methods

Annotate a bisulfite sequencing experiment (WGBS or RRBS) with probe weights and chromosomal position.

Description

Either: - Annotate a BSseq object with chromosome position and test statistic, or - Parse output from DSS::DMLtest() or DSS::DMLtest.multiFactor() into a CpGannotated object.

Usage

sequencing.annotate(obj, methdesign, all.cov=FALSE, contrasts = FALSE, 
                                cont.matrix = NULL, fdr = 0.05, coef, ...) 

Arguments

obj	A BSseq object or data.frame output from DSS::DMLtest() or DSS::DMLtest.multiFactor().
methdesign	Methylation study design matrix describing samples and groups. Use of edgeR::modelMatrixMeth() to make this matrix is highly recommended, since it transforms a regular model.matrix (as one would construct for a microarray or RNA-Seq experiment) into a “two-channel” matrix representing methylated and unmethylated reads for each sample. Only applicable when obj is a BSseq object.
all.cov	If TRUE, only CpG sites where all samples have > 0 coverage will be retained. If FALSE, CpG sites for which some (not all) samples have coverage=0 will be retained.
contrasts	Logical denoting whether a limma-style contrast matrix is specified. Only applicable when obj is a BSseq object.
cont.matrix	Limma-style contrast matrix for explicit contrasting. For each call to sequencing.annotate, only one contrast will be fit. Only applicable when obj is a BSseq object.
fdr	FDR cutoff (Benjamini-Hochberg) for which CpG sites are individually called as significant. Used to index default thresholding in dmrcate(). Highly recommended as the primary thresholding parameter for calling DMRs. Only applicable when obj is a BSseq object.
coef	The column index in design corresponding to the phenotype comparison. Corresponds to the comparison of interest in design when contrasts=FALSE, otherwise must be a column name in cont.matrix. Only applicable when obj is a BSseq object.
...	Extra arguments passed to the limma function lmFit(). Only applicable when obj is a BSseq object.

Value

A CpGannotated-class.

Author(s)

Tim J. Peters <[e-mail]>

References

Peters, T. J., Buckley, M.J., Chen, Y., Smyth, G.K., Goodnow, C. C. and Clark, S. J. (2021). Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate. Nucleic Acids Research, 49(19), e109.

Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43(7), e47.

Examples

library(ExperimentHub)
library(SummarizedExperiment)
library(bsseq)
library(GenomeInfoDb)
eh = ExperimentHub()
bis_1072 <- eh[["EH1072"]]
pData(bis_1072) <- data.frame(replicate=gsub(".*-", "", colnames(bis_1072)),
                   tissue=substr(colnames(bis_1072), 1, nchar(colnames(bis_1072))-3), 
                   row.names=colnames(bis_1072))
colData(bis_1072)$tissue <- gsub("-", "_", colData(bis_1072)$tissue)
bis_1072 <- renameSeqlevels(bis_1072, mapSeqlevels(seqlevels(bis_1072), "UCSC"))
bis_1072 <- bis_1072[seqnames(bis_1072)=="chr19",]
bis_1072 <- bis_1072[240201:240300,]
tissue <- factor(pData(bis_1072)$tissue)
tissue <- relevel(tissue, "Liver_Treg")
design <- model.matrix(~tissue)
colnames(design) <- gsub("tissue", "", colnames(design))
colnames(design)[1] <- "Intercept"
rownames(design) <- colnames(bis_1072)
methdesign <- edgeR::modelMatrixMeth(design)
cont.mat <- limma::makeContrasts(treg_vs_tcon=Lymph_N_Treg-Lymph_N_Tcon,
                                 fat_vs_ln=Fat_Treg-Lymph_N_Treg,
                                 skin_vs_ln=Skin_Treg-Lymph_N_Treg,
                                 fat_vs_skin=Fat_Treg-Skin_Treg,
                                 levels=methdesign)
seq_annot <- sequencing.annotate(bis_1072, methdesign, all.cov = TRUE, 
                                   contrasts = TRUE, cont.matrix = cont.mat, 
                                   coef = "treg_vs_tcon", fdr=0.05)

timpeters82/DMRcate-devel documentation built on Dec. 19, 2024, 11:14 a.m.