Skip to content

How do you derive ProbeAnnotation in MethylMix packages? #7

Description

@Yunuuuu

Hi, I came across methylmix algorithm, I wanted to integrate multiple probe methylation values mapping to one gene into gene methylation level. methylmix clusters multiple probe methylation value with a probe annotation data, I have read methylmix citation articles, 1 and 2, but I didn't find where the annotation data came from, and I checked it by below code:

library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(MethylMix)
library(tidyverse)

probe_with_one_more_gene <- Other$UCSC_RefGene_Name %>%
  purrr::map( ~unique(str_split(., pattern = ";")[[1]]) ) %>%
  purrr::map_lgl(
    ~length(.) >= 2
  ) %>%
  {rownames(Other)[.]}


anno_diff <- inner_join(
  ProbeAnnotation,
  as_tibble(Other, rownames = "ILMNID") %>%
    dplyr::select(ILMNID, UCSC_RefGene_Name, UCSC_RefGene_Group),
  by = "ILMNID"
) %>%
  dplyr::filter(
    ILMNID %in% probe_with_one_more_gene
  )


head(anno_diff)

here is the output:

      ILMNID   GENESYMBOL   UCSC_RefGene_Name UCSC_RefGene_Group
1 cg00050873        TSPY4      TSPY4;FAM197Y2       Body;TSS1500
2 cg00061679         DAZ1      DAZ1;DAZ4;DAZ4     Body;Body;Body
3 cg00311963 LOC100101121 LOC100101121;TTTY23    TSS1500;TSS1500
4 cg00335297       RBMY1F      RBMY1F;RBMY2FP    TSS1500;TSS1500
5 cg00576139 LOC100101115 LOC100101115;TTTY21          Body;Body
6 cg00903245        TSPY4      TSPY4;FAM197Y2          Body;Body

Could you explain how to deal with the multiple mapping to gene name of a single probe ID? It seems ProbeAnnotation just takes the first one?

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions