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README.Rmd
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---
output:
md_document:
variant: markdown_github
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# seqMeta
[](https://travis-ci.org/DavisBrian)
[](https://ci.appveyor.com/project/DavisBrian/seqMeta)
[](http://cran.r-project.org/web/packages/seqMeta)
Meta-Analysis of Region-Based Tests of Rare DNA Variants
Computes necessary information to meta analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies, and performs meta analysis.
## You can install:
* the latest released version from CRAN with
```R
install.packages("seqMeta")
```
* the latest development version from github with
```R
if (packageVersion("devtools") < 1.6) {
install.packages("devtools")
}
devtools::install_github("DavisBrian/seqMeta")
```
If you encounter a clear bug, please file a minimal reproducible example on [github](https://github.com/DavisBrian/seqMeta/issues).
## seqMeta 1.6.0
* Migrated to git / github
+ Bug Reports and Feature Requests should be submitted [github](https://github.com/DavisBrian/seqMeta/issues).
* Minimum R version moved to 3.1.0
* Duplicated SNP in snpinfo gene no longer pulls from the genotype matrix twice.
* Monomorphic snps with caf != 0 were handled incorrectly.
* Binomial models when genotypes imputed outside of seqMeta did not match when models were imputed by seqMeta. Very slight differences in the covariance structure.
* Replaced `any(is.na(Z))` with `anyNA(Z)`
* Range test now checks that genotypes are [0, 2].
* SNPInfo in seqMetaExamples had incorrect type of snpNames and aggregateBy.
* Automatically convert (with warning) aggregateBy and snpName columns to type character if they are not already.
* Added new function prepScores2
### prepScores2
prepScores2 is a drop in replacement for prepScores, prepScoresX and prepCox. The only difference is the family argument should be text. `gaussian()` becomes `"gaussian"`, `binomial()` becomes `"binomial"` and `"cox"` is used for survival models. prepScores2 is much faster in cases where genotype imputation occurs.
* 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