Lack of LUSC methylation data in SE object

Question

[aUser]

Hi, I am working on TCGA-LUSC methylation analysis using TCGABiolinks, but I am unable to find out the groupCol and groups for differential methylation analysis (for TCGAanalyze_DMC function). When I looked into the object, it contains no info regarding methylation. My sequence of commands is as:

query.met.lusc <- GDCquery(
    project = "TCGA-LUSC", 
    data.category = "DNA Methylation", 
    data.type = "Methylation Beta Value",
    platform = "Illumina Human Methylation 450",
    workflow = "SeSAMe Methylation Beta Estimation" )

GDCdownload(query.met.lusc)

lusc.met <- GDCprepare(
    query = query.met.lusc,
    save = FALSE)

There is no error while executing the above commands.

If I compare TCGA-LUAD and TCGA-LUSC SE objects, LUAD has 87 columns of data, while LUSC has 81 (methylation is at the 84th position). So I suspect that something went wrong during GDCPrepare() step, but I am unable to figure it out.

Any help or clue in this regard is highly appreciated.

Rv4.2.1, TCGABiolinks v2.25.3

Answer 1

[aUser]

I could not find the answer to this query, however, I got a better approach using DML in Sesame package.

A relevant tutorial can be found here:

https://www.bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/modeling.html#DMR

If someone else happens to be stuck on this issue:

CIMP: CpG island methylation phenotype; CIMP-Low 1/5 to 3/5 methylated CpGs, CIMP-High, >4/5 methylated CpGs

CpG island Defined as regions of >500 bp with >55% of GC content and expected/observed CpG ratio of >0.65. 40% of gene promoters contain islands.