IMAGE is implemented as an open source R package for mQTL mapping in sequencing-based methylation studies. IMAGE properly accounts for the count nature of bisulfite sequencing data and incorporates allele-specific methylation patterns from heterozygous individuals to enable more powerful mQTL discovery.
IMAGE jointly accounts for both allele-specific methylation information from heterozygous individuals and non-allele-specific methylation information across all individuals, enabling powerful ASM-assisted mQTL mapping. In addition, IMAGE relies on an over-dispersed binomial mixed model to directly model count data, which naturally accounts for sample non-independence resulting from individual relatedness, population stratification, or batch effects that are commonly observed in sequencing studies.IMAGE can identify 50%-64% more mQTL than existing approaches.
Cite
Fan, Y., Vilgalys, T. P., Sun, S., Peng, Q., Tung, J., & Zhou, X. (2019). High-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis. bioRxiv, 615039.
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