Commit ccab5432 authored by Edi Prifti's avatar Edi Prifti

migrating to mac

parent 7035effb
......@@ -5,7 +5,7 @@
#' @name cir_train
#' @title Cirhosis stage 1 (frequencies)
#' @docType data
#' @author Qin, Nan, Fengling Yang, Ang Li, Edi Prifti, Yanfei Chen, Li Shao, Jing Guo, et al “Alterations of the human gut microbiome in liver cirrhosis.” Nature 513, no. 7516 (July 23, 2014): 59–64.
#' @author Qin, Nan, Fengling Yang, Ang Li, Edi Prifti, Yanfei Chen, Li Shao, Jing Guo, et al “Alterations of the human gut microbiome in liver cirrhosis.” Nature 513, no. 7516 (July 23, 2014): 59–64 _.
#' @keywords liver cirrhosis, microbiome, species
#' @description This dataset consists of frequency abundance files as downloaded from http://waldronlab.io/curatedMetagenomicData/.
#' This is a list containing two elements: (i) the X data matrix with 1045 species and 181 observations and (ii) patient class = -1 (n=98) and healthy controls (n=83)
......
......@@ -50,11 +50,11 @@ t2dw$y <- data.karlsson.bug.y
save(t2dw, file="t2dw.rda", compress = TRUE, compression_level = 9)
rm(list=ls()); gc()
# (7) cirrhosis stage 1 counts
load("/data/projects/predomics_testing/data/segata_2017/data.bugs/qinn_bug_stage1.rda")
cir_train_count <- list()
cir_train_count$X <- as.data.frame(data.qinn.bug.stage1.counts.species); dim(cir_train_count$X) # 1045 181
cir_train_count$y <- data.qinn.bug.y
save(cir_train_count, file="cir_train_count.rda", compress = TRUE, compression_level = 9)
rm(list=ls()); gc()
# # (7) cirrhosis stage 1 counts
# load("/data/projects/predomics_testing/data/segata_2017/data.bugs/qinn_bug_stage1.rda")
# cir_train_count <- list()
# cir_train_count$X <- as.data.frame(data.qinn.bug.stage1.counts.species); dim(cir_train_count$X) # 1045 181
# cir_train_count$y <- data.qinn.bug.y
# save(cir_train_count, file="cir_train_count.rda", compress = TRUE, compression_level = 9)
# rm(list=ls()); gc()
......@@ -15,6 +15,5 @@ LaTeX: pdfLaTeX
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageBuildArgs: --resave-data
PackageCheckArgs: --as-cran
PackageRoxygenize: rd,collate,namespace
......@@ -48,12 +48,47 @@ A *predomics* model is coded in R as a S3 object, which contains a certain numbe
# Getting started
\
# Installing and loading `predomics`
\
`predomics` package is available on Integromics' GitLab and can be installed on your computer through the following instructions:
```{r, warning=FALSE, echo=T, message=F}
# Load "devtools" library (install it if needed)
ip <- installed.packages()
if(!("devtools" %in% rownames(ip)))
{
install.packages("devtools")
}
library(devtools)
if(!("predomics" %in% rownames(ip)))
{
#creds = git2r::cred_user_pass("eprifti", getPass::getPass())
creds = git2r::cred_ssh_key("/home/eprifti/.ssh/id_rsa.pub",
"/home/eprifti/.ssh/id_rsa")
# Install "predomics" from the gitlab
install_git(url = "https://git.integromics.fr/Predomics/predomics",
credentials = creds
)
rm(creds)
}
# load the library
library(predomics)
rm(ip)
```
## Setting the environment
In this example we will use data from the package
```{r}
data(cir1)
data(package = "predomics")
data("cir_train")
data("cir_test")
# # take out the lines with zero signal
#
......
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