can "is.na" expression be part of a query for subsetMaf?

PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

http://bioconductor.org/packages/release/bioc/html/maftools.html

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can "is.na" expression be part of a query for subsetMaf? #1002

Closed xguijarro closed 5 months ago

xguijarro commented 8 months ago

Hello, I am trying to filter my variants based on population allele frequency with subsetMaf, but I cannot figure out how to keep all those variants without a value for gnomAD_AF . If I try: subsetMaf(maf = aml, query = (is.na("gnomAD_AF") | "gnomAD_AF < 0.1")) And get this error: Error in is.na("gnomAD_AF") | "gnomAD_AF < 0.1" : operations are possible only for numeric, logical or complex types

Any ideas will be really appreciated :)

R version 4.3.1 maftools_2.18.0

github-actions[bot] commented 6 months ago

This issue is stale because it has been open for 60 days with no activity.

github-actions[bot] commented 5 months ago

This issue was closed because it has been inactive for 14 days since being marked as stale.