Package 'scRNAseqApp'

Class "APPconf"

Description

An object of class "APPconf" represents the metadata for a dataset.

Usage

APPconf(...)

Arguments

...	Each argument in ... becomes an slot in the new "APPconf"-class.

Value

A APPconf object.

Slots

title

character(1). Title of the data

id

character(1). Folder name of the data

species

character(1). species

ref

Reference information in a list with element bib, doi, pmid and entry. Entry must be an object of bibentry

type

character(1). Type of the data, scRNAseq or scATACseq.

markers

list. A list of data.frame represents cell markers.

keywords

character. A vector of characters represents the keywords of the study.

groupCol

character. The key group column name to separate the cells.

Examples

appconf <- readRDS(system.file("extdata", "data",
    "pbmc_small", "appconf.rds", package="scRNAseqApp"))
appconf

---

The methods for APPconf-class

Description

The assessment and replacement methods for APPconf-class

Usage

## S4 method for signature 'APPconf'
show(object)

## S4 method for signature 'APPconf'
x$name

## S4 replacement method for signature 'APPconf'
x$name <- value

## S4 method for signature 'APPconf,ANY,ANY'
x[[i, j, ..., exact = TRUE]]

## S4 replacement method for signature 'APPconf,ANY,ANY,ANY'
x[[i, j, ...]] <- value

## S4 method for signature 'APPconf,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'APPconf'
as.list(x, ...)

## S4 method for signature 'APPconf'
as.character(x, ...)

## S4 method for signature 'APPconf'
markers(x)

## S4 method for signature 'APPconf'
lapply(X, FUN, ...)

## S4 method for signature 'APPconf'
unlist(x, recursive = TRUE, use.names = TRUE)

Arguments

object	an object of APPconf
x	APPconf object.
name	A literal character string or a name (possibly backtick quoted).
value	value to replace.
i, j	indices specifying elements to extract or replace.
...	Named or unnamed arguments to form a signature.
exact	see Extract
drop	see drop
X	an APPconf cobject.
FUN	function used by lapply
recursive, use.names	function used by unlist

Value

A named character vector.

Examples

appconf <- readRDS(system.file("extdata", "data",
    "pbmc_small", "appconf.rds", package="scRNAseqApp"))
appconf
appconf$title
appconf[["title"]]
as.list(appconf)
as.character(appconf)
markers(appconf)
lapply(appconf, print)
unlist(appconf)

---

Create a metadata to describe the dataset

Description

The function will return a APPconf object which contain the reference, keywords for the dataset.

Usage

createAppConfig(
  title,
  destinationFolder,
  species,
  doi,
  pmid,
  bibentry,
  datatype = c("scRNAseq", "scATACseq", "scMultiome"),
  markers,
  keywords,
  abstract
)

Arguments

title	The title of the dataset
destinationFolder	The destination folder name of the dataset without the root folder of the datasets. The data will be saved as appdataFolder/destinationFolder
species	The species of the dataset
doi, pmid	The DOI or PMID of the reference
bibentry	An object of bibentry
datatype	character(1). Type of the data, scRNAseq, scATACseq or scMultiome.
markers	A list of data.frame with gene symbols as rownames or a character vector.
keywords	The keywords for the dataset. For example the condition, cell type, tissue information The keywords will be used for whole database search
abstract	The abstract of the reference.

Value

An object of APPconf object

Examples

if(interactive()){
    config <- createAppConfig(
        title="pbmc_small",
        destinationFolder = "pbmc_small",
        species = "Homo sapiens",
        doi="10.1038/nbt.3192",
        datatype = "scRNAseq")
}

---

Create a dataset Create a dataset from a Seurat object. The function will try to find the markers in the Misc data named as 'markers'. The misc data should be output of function FindAllMarkers.

Description

Create a dataset Create a dataset from a Seurat object. The function will try to find the markers in the Misc data named as 'markers'. The misc data should be output of function FindAllMarkers.

Usage

createDataSet(
  appconf,
  seu,
  config,
  contrast,
  assayName,
  gexSlot = c("data", "scale.data", "counts"),
  atacAssayName,
  atacSlot = c("data", "scale.data", "counts"),
  LOCKER = FALSE,
  datafolder = "data",
  default.symbol = "rownames",
  binSize = 1,
  fragmentNameMapList
)

Arguments

appconf	a list object represent the information about the dataset
seu	a Seurat object
config	config file for makeShinyFiles
contrast	The contrast group
assayName	assay in single-cell data object to use for plotting gene expression, which must match one of the following: Seurat objects: "RNA" or "integrated" assay, default is "RNA"
gexSlot	layer in single-cell assay to plot. Default is to use the "data" layer
atacAssayName	assay in single-cell data object to use for plotting open chromatin.
atacSlot	layer in single-cell atac assay to plot. Default is to use the "data" layer
LOCKER	Set locker if the file is required login
datafolder	app data folder
default.symbol	character(1L) specifying the default rownames to be used. If use default, the gene symbols will be the row names of the assay. If one column name of the meta.feature of the assay is supplied, the function will try to extract the symbols from the meta.feature slot of the assay.
binSize	number of bps for each bin for ATAC fragment coverage. Used to reduce the file size of bigwig.
fragmentNameMapList	list of named character vector. The name map list must be the same order as the fragment list in the object. For each element of the list, the names of the vector are the name of the fragment and the vector contains the cell names (column names of the assay).

Value

The updated Seurat object.

Examples

library(Seurat)
if(interactive()){
    appconf <- createAppConfig(
        title="pbmc_small",
        destinationFolder = "pbmc_small",
        species = "Homo sapiens",
        doi="10.1038/nbt.3192",
        datatype = "scRNAseq")
    createDataSet(appconf, pbmc_small, datafolder=tempdir())
}

---

load data from cellRanger

Description

load data from cellRanger

Usage

createSeuFromCellRanger(outsFolder)

Arguments

outsFolder

the outs folder of cellRanger

Value

An SeuratObject

---

load data from a count matrix

Description

load data from a count matrix

Usage

createSeuFromMatrix(matrix, meta, genes, cluster, ...)

Arguments

matrix	count matrix
meta	cell-level meta data
genes	character. gene names, will be the rownames of the matrix
cluster	the cluster coordinates
...	The parameter passed to read.delim when read cluster file.

Value

An SeuratObject

---

Create a scRNAseqApp project

Description

To run scRNAseqApp, you need to first create a directory which contains the required files.

Usage

scInit(
  app_path = getwd(),
  root = "admin",
  password = "scRNAseqApp",
  datafolder = "data",
  overwrite = FALSE,
  app_title = "scRNAseq Database",
  app_description =
    "This database is a collection of\n        single cell RNA-seq data.",
  passphrase = NULL
)

Arguments

app_path	path, a directory where do you want to create the app
root	character(1), the user name for administrator
password	character(1), the password for administrator
datafolder	the folder where saved the dataset for the app
overwrite	logical(1), overwrite the app_path if there is a project.
app_title, app_description	character(1). The title and description of the home page.
passphrase	A password to protect the data inside the database.

Value

no returns. This function will copy files to app_path

Examples

if(interactive()){
    scInit()
}

---

scRNAseqApp main function

Description

create a scRNAseqApp once the initialization is done.

Usage

scRNAseqApp(
  app_path = getwd(),
  datafolder = "data",
  defaultDataset = "pbmc_small",
  windowTitle = "scRNAseq/scATACseq database",
  favicon = system.file("assets", "img", "favicon.ico", package = "scRNAseqApp"),
  banner = system.file("assets", "img", "banner.png", package = "scRNAseqApp"),
  footer = tagList(HTML("©"), "2020 -", format(Sys.Date(), "%Y"), "jianhong@duke"),
  maxRequestSize = 1073741824,
  timeout = 30,
  theme = bs_theme(bootswatch = "lumen"),
  use_bs_themer = FALSE,
  showHelpVideo = FALSE,
  ...
)

Arguments

app_path	path, a directory where do you want to create the app
datafolder	the folder where saved the dataset for the app
defaultDataset	default dataset for the app.
windowTitle	The title that should be displayed by the browser window.
favicon	The favicon for the page.
banner	The banner image.
footer	The footer html contents.
maxRequestSize	Maximal upload file size. Default is 1G.
timeout	Timeout session (minutes) before logout if sleeping. Default to 30. 0 to disable.
theme	A theme.
use_bs_themer	logical(1). Used to determine the theme.
showHelpVideo	logical(1) or character(1). Show help videos in homepage or not. If an url is provided, the url will be embeded as a iframe element.
...	parameters can be passed to shinyApp except ui and server.

Value

An object that represents the app.

Examples

if(interactive()){
    app_path=tempdir()
    scInit(app_path=app_path)
    setwd(app_path)
    scRNAseqApp()
}

---