NAs in feature matrix

[jeinson]

When generating a matrix of features for RIVER, how do the developers handle situations where no variant near a particular gene has a CADD annotation for features like TFBS or EncOCCombPVal? glmnet cannot handle NAs, but n my dataset 95% of genes have at least one missing feature annotation, so removing such cases would waste most of the data.

Ex:

	cHmmTx	cHmmTssBiv	cHmmHet	cHmmBivFlnk	cHmmTxFlnk	TFBS	EncOCCombPVal
GTEX-111YS:ENSG00000007923	0.016	0	0	0	0.000	NA	NA
GTEX-117YW:ENSG00000007923	0.000	0	0	0	0.000	NA	NA
GTEX-1192X:ENSG00000007923	0.000	0	0	0	0.000	NA	NA
GTEX-11EM3:ENSG00000007923	0.000	0	0	0	0.008	NA	NA
GTEX-11EQ8:ENSG00000007923	0.000	0	0	0	0.000	NA	NA
GTEX-11EQ9:ENSG00000007923	0.016	0	0	0	0.000	NA	NA

[ipw012]

Especially for annotation from ENCODE like chromatin states and TFBS, there are many NAs. In those cases, we used a minimum number (0), which is background. This is also what CADD used in their variant feature imputations.