Package 'yulab.utils'

Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Authors: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <[email protected]>
License: Artistic-2.0
Version: 0.1.8.001
Built: 2024-12-03 10:32:30 UTC
Source: https://github.com/yulab-smu/yulab.utils

Help Index

c2

Description

chunked array

Usage

c2(x, y)

Arguments

x

a vector or chunked_array object
y

a vector or chunked_array object

Details

concate two vector/chunked_array into a chunked_array object

Value

chunked_array object

Author(s)

Guangchuang Yu

check_pkg

Description

Check whether the input packages are installed

Usage

check_pkg(pkg, reason = NULL, ...)

Arguments

pkg

package names
reason

the reason to check the pkg. If NULL, it will set the reason to the parent call.
...

additional parameters that passed to rlang::check_installed()

Details

This function check whether the input packages are installed. If not, it asks the user whether to install the missing packages.

Value

see also check_installed

Author(s)

Guangchuang Yu

combinations

Description

all possible combinations of n sets

Usage

combinations(n)

Arguments

n

number of sets

Value

a list of all combinations

print md text of package with link to homepage (CRAN or Bioconductor)

Description

print md text of package with link to homepage (CRAN or Bioconductor)

Usage

CRANpkg(pkg)

Biocpkg(pkg)

Arguments

pkg

package name

Value

md text string

Author(s)

Guangchuang Yu

exec

Description

run system command

Usage

exec(command)

Arguments

command

system command to run

Value

An exec instance that stores system command outputs

Author(s)

Guangchuang Yu

get_dependencies

Description

get reverse dependencies

Usage

get_dependencies(pkg, repo = c("CRAN", "BioC"))

Arguments

pkg

package name
repo

'CRAN' and/or 'BioC'

Value

reverse dependencies

Author(s)

Guangchuang Yu

get_fun_from_pkg

Description

load function from package

Usage

get_fun_from_pkg(pkg, fun)

Arguments

pkg

package
fun

function

Value

function

Author(s)

Guangchuang Yu

Examples

get_fun_from_pkg('utils', 'zip')

print md text of package with link to github repo

Description

print md text of package with link to github repo

Usage

Githubpkg(user, pkg)

Arguments

user

github user
pkg

package name

Value

md text string

Author(s)

Guangchuang Yu

has_internet

Description

test for internect connection via reading lines from a URL

Usage

has_internet(site = "https://www.baidu.com/")

Arguments

site

URL to test connection

Value

logical value

Author(s)

Guangchuang Yu

cache intermediate data

Description

Yulab provides a set of utilities to cache intermediate data, including initialize the cached item, update cached item and rmove the cached item, etc.

Usage

initial_cache()

get_cache()

rm_cache()

initial_cache_item(item)

get_cache_item(item)

rm_cache_item(item)

update_cache_item(item, elements)

get_cache_element(item, elements)

Arguments

item

the name of the cached item
elements

elements to be cached in the item

Value

return the cache environment, item or selected elements, depends on the functions.

Examples

## Not run: 
 slow_fib <- function(x) {
     if (x < 2) return(1)
     slow_fib(x-2) + slow_fib(x-1)
 }
 
 fast_fib <- function(x) {
     if (x < 2) return(1)
     res <- get_cache_element('fibonacci', as.character(x))
     if (!is.null(res)) { 
         return(res)
     }
     res <- fast_fib(x-2) + fast_fib(x-1)
     e <- list()
     e[[as.character(x)]] <- res
     update_cache_item('fibonacci', e)
     return(res)
 }

 system.time(slow_fib(30))
 system.time(fast_fib(30)) 
    
 
## End(Not run)

install_zip

Description

install R package from zip file of source codes

Usage

install_zip(file, args = "--no-build-vignettes")

Arguments

file

zip file
args

argument to build package

Value

No return value, called for install R package from zip file of source codes

Author(s)

Guangchuang Yu

install_zip_gh

Description

install github package

Usage

install_zip_gh(repo, ref = "HEAD", args = "--no-build-vignettes")

Arguments

repo

github repo
ref

github branch, default is HEAD, which means the default branch of the GitHub repo
args

argument to build package

Details

it download the zip file first and use install_zip to install it

Value

No return value, called for installing github package

Author(s)

Guangchuang Yu

is.installed

Description

Check whether the input packages are installed

Usage

is.installed(packages)

Arguments

packages

package names

Details

This function check whether the input packages are installed

Value

logical vector

Author(s)

Guangchuang Yu

Examples

is.installed(c("dplyr", "ggplot2"))

Convert a list of vector (e.g, gene IDs) to a data.frame object

Description

Convert a list of vector to a data.frame object.

Usage

ls2df(inputList)

Arguments

inputList

A list of vector

Value

a data.frame object.

mat2df

Description

convert a matrix to a tidy data frame (from wide to long format as described in the tidyverse concept)

Usage

mat2df(x)

Arguments

x

the input matrix

Value

a data.frame in long format with the 'value' column stores the original values and 'row' and 'col' columns stored in row and column index as in x

Author(s)

Guangchuang Yu

Examples

x <- matrix(1:15, nrow = 3)
mat2df(x)

mat2list

Description

convert a matrix to a list

Usage

mat2list(x)

Arguments

x

the input matrix

Value

a list that contains matrix columns as its elements

Examples

x <- matrix(1:15, nrow = 3)
mat2list(x)

mypkg

Description

print md text of link to a pakcage

Usage

mypkg(pkg, url)

Arguments

pkg

package name
url

package url

Value

md text string

Author(s)

Guangchuang Yu

o

Description

open selected directory or file

Usage

o(file = ".")

Arguments

file

to be open; open working directory by default

Value

No return value, called for opening specific directory or file

Author(s)

Guangchuang Yu

Examples

## Not run: 
## to open current working directory
o()

## End(Not run)

packageTitle

Description

Extract package title

Usage

packageTitle(pkg, repo = "CRAN")

Arguments

pkg

package name
repo

'CRAN' and/or 'BioC'

Value

reverse dependencies

Author(s)

Guangchuang Yu

pload

Description

loading a package

Usage

pload(package, action = "auto")

Arguments

package

package name
action

function used to install package. If 'action = "auto"', it will try to use 'BiocManager::install()' if it is available.

Details

The function use 'library()' to load the package. If the package is not installed, the function will try to install it before loading it.

Value

the selected package loaded to the R session

Author(s)

Guangchuang Yu

rbindlist

Description

rbind a list

Usage

rbindlist(x)

Arguments

x

a list that have similar elements that can be rbind to a data.frame

Value

data.frame

Author(s)

Guangchuang Yu

read.cb

Description

read clipboard

Usage

read.cb(reader = read.table, ...)

Arguments

reader

function to read the clipboard
...

parameters for the reader

Value

clipboard content, output type depends on the output of the reader

Author(s)

Guangchuang Yu

scale-range

Description

normalized data by range

Usage

scale_range(data)

Arguments

data

the input data.

Value

normalized data

Author(s)

Guangchuang Yu

download publication via scihub

Description

using scihub to download publication using doi

Usage

scihub_dl(doi, scihub = "sci-hub.tw", download = TRUE)

Arguments

doi

doi
scihub

scihub website
download

whether download the pdf file

Value

pdf url

Author(s)

Guangchuang Yu

switch regular expression style (PCRE vs TRE)

Description

The set_regexpr_style() allows user to specify which style to be used, while the auto_set_regexpr_style() automatically set the style depdending on the operating system (TRE for Windows and PCRE for other OSs (Linux and Mac)).

Usage

set_PCRE()

set_TRE()

use_perl()

set_regexpr_style(style)

auto_set_regexpr_style()

Arguments

style

one of 'PCRE' or 'TRE'

Details

set_PCRE() force to use PCRE style while set_TRE() force to use TRE.

Note that all these functions are not change the behavior of gsub() and regexpr(). The functions are just set a global option to store the user's choice of whether using perl = TRUE.

Users can access the option via use_perl() and pass the return value to gusb() or regexpr() to specify the style in use.

Value

logical value of whether use perl

Author(s)

Guangchuang Yu

References

https://stackoverflow.com/questions/47240375/regular-expressions-in-base-r-perl-true-vs-the-default-pcre-vs-tre

show_in_excel

Description

Open data frame in Excel. It can be used in pipe.

Usage

show_in_excel(.data)

Arguments

.data

a data frame to be open

Value

original .data

Author(s)

Guangchuang Yu

str_detect

Description

Detect the presentce/absence of a match

Usage

str_detect(string, pattern, negate = FALSE)

Arguments

string

input string
pattern

pattern to look for
negate

if TRUE, inverts the resulting boolen vector

Value

logical vector

Author(s)

Guangchuang Yu

str_extract

Description

Extract a substring using a pattern

Usage

str_extract(string, pattern)

Arguments

string

input string
pattern

a regular expression to describe the pattern to extracted from the 'string'

Value

substring

Author(s)

Guangchuang Yu

str_starts

Description

Detect the presence or absence of a pattern at the beginning or end of a string or string vector.

Usage

str_starts(string, pattern, negate = FALSE)

str_ends(string, pattern, negate = FALSE)

Arguments

string

input string
pattern

pattern with which the string starts or ends
negate

if TRUE, return non-matching elements

Value

a logical vector

Author(s)

Guangchuang Yu

str_wrap

Description

wraping long string to multiple lines

Usage

str_wrap(string, width = getOption("width"))

Arguments

string

input string
width

the maximum number of characters before wrapping to a new line

Value

update strings with new line character inserted

Author(s)

Guangchuang Yu

yread

Description

read file with caching

Usage

yread_tsv(
  file,
  reader = utils::read.delim,
  params = list(),
  cache_dir = tempdir()
)

yread(file, reader = readLines, params = list(), cache_dir = NULL)

Arguments

file

a file or url
reader

a function to read the 'file_url'
params

a list of parameters that passed to the 'reader'
cache_dir

a folder to store cache files. If set to NULL will disable cache.

Details

This function read a file (local or url) and cache the content.

Value

the output of using the 'reader' to read the 'file_url' with parameters specified by the 'params'

Author(s)

Yonghe Xia and Guangchuang Yu

yulab_msg

Description

Messages for R package developed by YuLab

Usage

yulab_msg(pkgname = NULL, n = 1)

Arguments

pkgname

package name
n

number of citation messages

Value

package message

Author(s)

Guangchuang Yu