Annotation of CpG, DMRs and DMPs with MethylKit and Genomation in R

Question

[egascon]

Hello,

I have performed a methylation analysis using the R packages MethylKit and Genomation. I followed all the steps and arrived at our final object, AnnotationByGeneParts, for CpGs, DMRs, and DMPs. This object provides information on the regions corresponding to promoters, introns, and exons for each case.

Question: To determine which genes correspond to each of these sites, we used the following function:

getAssociationWithTSS(myDiff.all.anot_titles)

This function returned the following results:

target.row dist.to.feature   feature.name feature.strand
4                1           10172 XR_009599096.1              -
41               2           13346 XR_009599057.1              -
2                3            7171 XR_009599078.1              -
3191             4             973 XR_006058999.1              +
6354             5            3564 XR_003587871.2              +

My question is as follows: Is it correct to say that if the TSS corresponds to "XR_009599096.1," the nearest gene to this CpG is the one associated with the transcript "XR_009599096.1"?

This is because the dist_tss_titles object provides the distance to the TSS for each CpG, but I'm uncertain whether the transcript name (e.g., "XR_009599096.1") directly indicates the gene associated with the CpG site. Should I assume that the CpG site marked by XR_009599096.1 is related to the gene corresponding to that transcript, or is there additional information needed to confirm this association?

I would appreciate any clarification or insights from the community on how to correctly interpret these results.

P.D: The specie is Ovis Aries (Genome assembly ARS-UI_Ramb_v3.0)

Thank you,

Kind regards