Nothing
## ----setup, include = FALSE-----------------------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.dim = c(7, 4)
)
library(isatabr)
op <- options(width = 100)
## ----read-----------------------------------------------------------------------------------------
## Read ISA-Tab files from directory.
isaObject1 <- readISATab(path = file.path(system.file("extdata/Atwell", package = "isatabr")))
## ----readZip--------------------------------------------------------------------------------------
## Read ISA-Tab files from directory.
isaObject2 <- readISATab(path = file.path(system.file("extdata", package = "isatabr")),
zipfile = "Atwell.zip")
## ----pathAccess-----------------------------------------------------------------------------------
## Access path for isaObjects
isaPath(isaObject1)
isaPath(isaObject2)
## ----studyAccess----------------------------------------------------------------------------------
## Access studies.
isaStudies <- study(isaObject1)
## Print study names.
names(isaStudies)
## Access study descriptors.
isaSDD <- sDD(isaObject1)
## Shows study descriptors for study GMI_Atwell_study.
isaSDD$GMI_Atwell_study
## ----osrAccess------------------------------------------------------------------------------------
(isaOSR <- oSR(isaObject1))
## ----osrUpdate------------------------------------------------------------------------------------
## Update version number.
isaOSR[1, "Term Source Version"] <- 24
## Update oSR in ISA object.
oSR(isaObject1) <- isaOSR
## Check the updated oSR.
oSR(isaObject1)
## ----getAssay-------------------------------------------------------------------------------------
## Inspect assay tab.
isaAFile <- aFiles(isaObject1)
head(isaAFile$a_study1.txt)
## ----procAssay------------------------------------------------------------------------------------
## Get assay tabs for isaObject1.
aTabObjects <- getAssayTabs(isaObject1)
## Process assay data.
isaDat <- processAssay(isaObject = isaObject1,
aTabObject = aTabObjects$s_study1.txt$a_study1.txt,
type = "derived")
## Display first rows and columns.
head(isaDat[, 1:10])
## ----readFaahko-----------------------------------------------------------------------------------
## Read ISA-Tab files for faahKO.
isaObject3 <- readISATab(path = file.path(system.file("extdata/faahKO", package = "isatabr")))
## ----processFaahko, message=FALSE, eval=requireNamespace("xcms")----------------------------------
## Get assay tabs for isaObject3.
aTabObjects3 <- getAssayTabs(isaObject3)
## Process assay data.
isaDat3 <- processAssay(isaObject = isaObject3,
aTabObject = aTabObjects3$s_Proteomic_profiling_of_yeast.txt$a_metabolite.txt,
type = "raw")
## Display output.
isaDat3
## ----write, eval=FALSE----------------------------------------------------------------------------
# ## Write content of ISA object to a temporary directory.
# writeISAtab(isaObject = isaObject1,
# path = tempdir())
## ----writeSub, eval=FALSE-------------------------------------------------------------------------
# ## Write investigation file.
# writeInvestigationFile(isaObject = isaObject1,
# path = tempdir())
#
# ## Write study file.
# writeStudyFiles(isaObject = isaObject1,
# studyFilenames = "s_study1.txt",
# path = tempdir())
#
# ## Write assay file.
# writeAssayFiles(isaObject = isaObject1,
# assayFilenames = "a_study1.txt",
# path = tempdir())
## ----winddown, include = FALSE------------------------------------------------
options(op)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.