Package: diffdriver 0.1.8

Siming Zhao

diffdriver: Identify differential selection

This package implements a statistical method to detect differential selection of somatic mutations under different environments

Authors:Siming Zhao [aut, cre], Jie Zhou [aut], Qirui Zhang [aut]

# Install 'diffdriver' in R:

install.packages('diffdriver', repos = c('https://szhaolab.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Last updated from:a47b7dd99b. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	ERROR	148
source / vignettes	OK	218
linux-release	ERROR	176
macos-release	ERROR	146
macos-oldrel	ERROR	166
windows-devel	ERROR	118
windows-release	ERROR	105
windows-oldrel	ERROR	126
wasm-release	OK	130

Help page	Topics
Add intercept, if have functtypecode, then code and move to the front. different from driverMAPS! only allows functtypecode =7 \|\|8 when functypecode is included in selectvars.	ddmcode
diffDriver model	ddmodel
diffDriver model only for binary phenotype.	ddmodel_binary
diffDriver model only for binary phenotype, assuming bmr the same across samples.	ddmodel_binary_simple
Run diffDriver with Input Files	diffdriver
gene level binomial test	genebinom
gene level fisher's exact test	genefisher
gene level logistic regression	genelr
gene level multiple linear regression	mlr
gene level multiple linear regression, correcting for total number of mutations	mlr.v2
optifix. Optimise with fixed parameters	optifix
plot phenotype, mutation and annotation for a gene across samples	plot_mut