In DavisBrian/Firth: Firth Test

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "NEWS-"
)

seqMeta 1.5.0.9000

• Migrated to git / github
• Minimum R version moved to 3.1.0
• Added new function prepScores2
• Added automated tests for prepSNPInfo and prepScores2

prepScores2

prepScores2 is a drop in replacement for prepScores. The only difference is the family argument should be text. gaussian() becomes "gaussian". Although the former will temporarily still work. Eventually I'd like to merge prepScoresX and prepCox into this function as 90+% of the code is the same.

• removes duplicate snp-gene pairs in SNPInfo (fixes issue #0001)
• enforces assumption that when a gene is being anlyzed the same snp can only be in that gene once (same snp can still be in multiple genes or in the same gene in SNPInfo)
• Reorganized code
• Moved data checks before imputation of genotypes
• Moved other checks closer to where the data is calculated / used
• Improved speed and reduced memory usage by
  • Replacing genotype imputation apply code with a faster vectorized version.
  • Replacing any(is.na(Z)) with anyNA(Z)
  • Replacing range with min and max
  • Replacing matrix operations of the form t(x)%*%y with crossprod(x, y)
  • Removing duplicate calculations
  • Removing orphaned code
  • Removing second imputation of genotypes in the covariance calculation
  • Converting genotype matrix of type data_frame to a matrix.
• Added Error Messages for
  • Missing weight for snp-gene pair
  • Duplicate weights for snp-gene pair
  • Non-numeric genotypes
  • family != gaussian or binomial
• Added Warning Messages for:
  • Removing missing snps and genes from SNPInfo
  • Removing duplicated snp-gene pairs

Todo

• change genotype documentation to "matrix or an object which can be coerced to one with as.matrix"
• add back verbose option to prepScores2
• prepScores2 support for male
• prepScores2 support for Survival
• check kins and Z are in the same order?
• need to verify impute_to_mean code does NOT make a copy of the genotype matrix if it is a matrix
• add prepSNPInfo to other prep Functions and the Meta functions to close out issue #0001
• test real binomial cases
• test real kinship cases

DavisBrian/Firth documentation built on May 6, 2019, 1:55 p.m.