Question: DNA methylation analysis without raw data IDAT files
0
gravatar for Beginner
13 months ago by
Beginner50
Beginner50 wrote:

Hi,

I'm interested in working on DNA methylation data. I have downloaded TCGA data from GDC harmonised archive. There are no IDAT files. 

IDAT files are available only for GDC legacy archive. 

Dataframe "data" is with 485577 probes as rows and 439 columns. There are columns like Chromosome, Start position, End position, Gene and Samples with values for each probe.

For eg it looks like below:

        Chr    Start    End    Gene    GeneType    TranscriptID    TCGA-DD-A3A3-01A    TCGA-G3-AAV1-01A    TCGA-DD-AACX-01A    TCGA-DD-A4NI-01A    TCGA-G3-AAV4-01A    TCGA-DD-A1EG-11A
    cg00000029    chr16    53434200    53434201    RBL2    protein_coding    ENST00000262133.9    0.550913627    0.390846294    0.210664637    0.329930064    0.193362596    0.309831311
    cg00000108    chr3    37417715    37417716    C3orf35    lincRNA    ENST00000328376.8    NA    NA    NA    NA    NA    NA
    cg00000109    chr3    172198247    172198248    FNDC3B    protein_coding    ENST00000336824.7    NA    NA    NA    NA    NA    NA
    cg00000165    chr1    90729117    90729118    .    .    .    0.570880538    0.074518375    0.174949392    0.136944673    0.064590585    0.151404705
    cg00000236    chr8    42405776    42405777    VDAC3    protein_coding    ENST00000022615.7    0.914067333    0.845768766    0.901394742    0.922730081    0.910097231    0.887756996

I have seen many R packages like mini, Champ, miss methyl etc....But all the packages can be used only with IDAT files. And I'm not aware about how I can do the methylation analysis with data in a dataframe.

Any help is appreciated. 

ADD COMMENTlink modified 13 months ago by Yuan Tian120 • written 13 months ago by Beginner50
Answer: DNA methylation analysis without raw data IDAT files
0
gravatar for James W. MacDonald
13 months ago by
United States
James W. MacDonald51k wrote:

?readTCGA in minfi may be helpful here.

ADD COMMENTlink written 13 months ago by James W. MacDonald51k

Hi James,

I tried reading the methylation data with readTCGA. But it is not working. May be I'm wrong somewhere

The methylation data is in a dataframe "df" with rows as probes and columns like Chromosome, Start position, End position, Gene and Samples like mentioned in my question. 

library(minfi)
readTCGA(df)

This gave an error like below: 

Error in readLines(filename, n = 2) : 'con' is not a connection

Could you please show me an example. Thank you

 

 

ADD REPLYlink modified 13 months ago • written 13 months ago by Beginner50

Most help pages have an example, and readTCGA is no different. You can't just use a function without reading the help page, and if you had read the help page you wouldn't have tried to do what you did.

If you are planning to get anywhere with R and/or Bioconductor, you will need to become more self-sufficient. You either need to learn how to figure things out for yourself, by reading the help pages and vignettes and googling for answers, or you need to find somebody local who has the skills to do the work for you. Just trying something random and then asking for help on this support site isn't a good long term strategy.

ADD REPLYlink written 13 months ago by James W. MacDonald51k
Answer: DNA methylation analysis without raw data IDAT files
0
gravatar for Yuan Tian
13 months ago by
Yuan Tian120
University College London
Yuan Tian120 wrote:

Actually ChAMP can do analysis with simple beta matrix and pheno vector, it's not relying on IDAT file. So if you can extract beta information from your file into proper matrix, you can then use ChAMP for all following analysis. But ChAMP does not provide loading function from your file format to R session.

Best

Yuan Tian

ADD COMMENTlink written 13 months ago by Yuan Tian120

yes, I didn't find anything to read methylation data from matrix with champ. Any idea about any other functions?

ADD REPLYlink written 13 months ago by Beginner50
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