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Cell population estimation

AM Amanda Mok
OS Olivia Solomon
RN Renuka R Nayak
PC Patrick Coit
HQ Hong L Quach
JN Joanne Nititham
AS Amr H Sawalha
LB Lisa F Barcellos
LC Lindsey A Criswell
SC Sharon A Chung
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DNA methylation patterns can vary between different blood cell populations.13 In order to account for cell-type heterogeneity between samples, we calculated principal components using the ReFACTor method14 to be used in multivariable regression. ReFACTor is a reference-free method that performs a principal component analysis (PCA) on the subset of CpG sites that are differentially methylated across different cell types to adjust for variance due to cell-type heterogeneity. We included the first two ReFACTor principal components in regression analyses to adjust for cell heterogeneity based on the examination of quantile-quantile plots for inflation and deflation of p values and calculation of genomic inflation factors (λ=0.90 for the first two principal components).

Copyright and License information:  ©2016-12-07 Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/
This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/

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