DNAm matrix for EUGEI

[SiyiSEA]

No description provided.

[SiyiSEA]

Download the DNAm from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152026.

There are three files under this link, but I will use the first one GSE152026_EUGEI_processed_signals.csv.gz

The dim of the file is 1869*860964.

The colnames are like this: 200889820113_R06C01, 200889820113_R06C01_Detection_Pval, 200864580076_R08C01, 200864580076_R08C01_Detection_Pval.

A pair of sample and pval.

[SiyiSEA]

I've tried to match the DNAm_processed_signal with the EUGEI_Methylation_Samples_PostQC_OUT.fam based on the sample names.

Hoever, there is no overlapped sample between these two files!!!

I've check if there is any other files under the path of /lustre/projects/Research_Project-MRC190311/SNPArray/sczMrcBlood/EUGEI can be matched in the DNAm_processed_signal.csv.

No - EUGEI_GROUP_EuroOnly_PCs_NonRefPanel_Dec17.txt
No - EUGEI_SNP_genotypes_matchedIDs.csv

[SiyiSEA]

Making a DNAm matrix for EUGEI needs four key files.

1. fam file EUGEI_Methylation_Samples_PostQC_OUT.fam
2. pheno file CombinedEuGEISamplesPassedQC.csv
3. meta file EUGEI_SNP_genotypes_matchedIDs.csv
4. DANm matrix GSE152026_EUGEI_processed_signals.csv

The relationship among these files:

1. V1 and V2 in the fam file <---> the Geno.Plate.ID in the meta file;
2. Sample.Name in the meta file <---> Eilis.Sample.Name in the pheno file;
3. Basename in the pheno file <---> colname of DNAm

What I did in the EUGEI_DNAm_pheno.R:

1. filter pheno file by remove samples without age and sex - 1067 left;
2. match pheno and DNAm based on the matched Sample.Name - 928 left;
3. rename the Sample.Name and remove the . and - in the name as SampleID;
4. apply the SampleID into covar, DNAm and fam.

There are four files been created:

1. covariates.txt which contains IID, Sex, Age and Silde_factor;
2. methylation.RData which contains DNAm data for 42588 probes and 928 samples;
3. keep_928_EUGEI.txt contains 928 samples for updating the plink file;
4. update_sampleID_EUGEI.txt contains the old sample name and the new sample name for updating the fam file;