mteb/BrightProStackoverflowRetrieval huggingface dataset:
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[ micropan  (version  1.0  ) ](/packages/micropan/versions/1.0)

#  readHmmer: Reading results from a HMMER3 scan

##  Description

Reading a text file produced by ` [ hmmerScan
](/link/hmmerScan?package=micropan&version=1.0) ` .

##  Usage

    
    
    readHmmer(hmmer.file,e.value=1,use.acc=TRUE)

##  Arguments

hmmer.file

The name of a ` [ hmmerScan ](/link/hmmerScan?package=micropan&version=1.0) `
result file.

e.value

Numeric threshold, hits with E-value above this are ignored (default is 1.0).

use.acc

Logical indicating if accession numbers should be used to identify the hits.

##  Value

The results are returned in a  data.frame  with columns  Query  ,  Hit  ,
Evalue  ,  Score  ,  Start  ,  Stop  ,  Description  .  Query  is the tag
identifying each sequence in each genome, typically  GID111_seq1  ,
GID121_seq3  , etc.  Hit  is the name or accession number for a pHMM in the
database describing patterns. The  Evalue  is the  ievalue  in the HMMER3
terminology. The  Score  is the HMMER3 score for the match between  Query  and
Hit  . The  Start  and  Stop  are the positions within the  Query  where the
Hit  (pattern) starts and stops.  Description  is the description of the  Hit
.There is one line for each hit.

##  Details

The function reads a text file produced by ` [ hmmerScan
](/link/hmmerScan?package=micropan&version=1.0) ` . By specifying a smaller
e.value  you filter out poorer hits, and fewer results are returned. The
option  use.acc  should be turned off (FALSE) if you scan against your own
database where accession numbers are lacking.

##  See Also

` [ hmmerScan ](/link/hmmerScan?package=micropan&version=1.0) ` , ` [
hmmerCleanOverlap ](/link/hmmerCleanOverlap?package=micropan&version=1.0) ` ,
` [ dClust ](/link/dClust?package=micropan&version=1.0) ` .

##  Examples

[ Run this code
](https://www.datacamp.com/datalab/preview?_tag=rdocs&rdocsPath=packages%2Fmicropan%2Fversions%2F1.0%2Ftopics%2FreadHmmer&utm_source=r-docs&utm_medium=docs&utm_term=readHmmer&utm_content=run_example_in_datalab)

    
    
    # See the example in the Help-file for dClust
    

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[ base  (version  3.6.2  ) ](/packages/base/versions/3.6.2)

#  body: Access to and Manipulation of the Body of a Function

##  Description

Get or set the body of a function.

##  Usage

    
    
    body(fun = sys.function(sys.parent()))
    body(fun, envir = environment(fun)) <- value

##  Arguments

fun

a function object, or see ‘Details’.

envir

environment in which the function should be defined.

value

an object, usually a [ language object
](/link/language%20object?package=base&version=3.6.2) : see section ‘Value’.

##  Value

` body ` returns the body of the function specified. This is normally a [
language object ](/link/language%20object?package=base&version=3.6.2) , most
often a call to ` { ` , but it can also be an object (e.g., ` pi ` ) to be the
return value of the function.

The replacement form sets the body of a function to the object on the right
hand side, and (potentially) resets the environment of the function. If `
value ` is of class ` " [ expression
](/link/expression?package=base&version=3.6.2) " ` the first element is used
as the body: any additional elements are ignored, with a warning.

##  Details

For the first form, ` fun ` can be a character string naming the function to
be manipulated, which is searched for from the parent frame. If it is not
specified, the function calling ` body ` is used.

The bodies of all but the simplest are braced expressions, that is calls to `
{ ` : see the ‘Examples’ section for how to create such a call.

##  See Also

` [ alist ](/link/alist?package=base&version=3.6.2) ` , ` [ args
](/link/args?package=base&version=3.6.2) ` , ` [ function
](/link/function?package=base&version=3.6.2) ` .

##  Examples

[ Run this code
](https://app.datacamp.com/workspace/preview?_tag=rdocs&rdocsPath=packages%2Fbase%2Fversions%2F3.6.2%2Ftopics%2Fbody&utm_source=r-docs&utm_medium=docs&utm_term=body&utm_content=run_example_in_workspace)

    
    
    # NOT RUN {
    body(body)
    f <- function(x) x^5
    body(f) <- quote(5^x)
    ## or equivalently  body(f) <- expression(5^x)
    f(3) # = 125
    body(f)
    
    ## creating a multi-expression body
    e <- expression(y <- x^2, return(y)) # or a list
    body(f) <- as.call(c(as.name("{"), e))
    f
    f(8)
    # }
    # NOT RUN {
    <!-- %% Rd parser bug? : need to backslash-escape the "{" below: -->
    # }
    # NOT RUN {
    ## Using substitute() may be simpler than 'as.call(c(as.name("{",..)))':
    stopifnot(identical(body(f), substitute({ y <- x^2; return(y) })))
    # }
    

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[ base  (version  3.6.2  ) ](/packages/base/versions/3.6.2)

#  eapply: Apply a Function Over Values in an Environment

##  Description

` eapply ` applies ` FUN ` to the named values from an ` [ environment
](/link/environment?package=base&version=3.6.2) ` and returns the results as a
list. The user can request that all named objects are used (normally names
that begin with a dot are not). The output is not sorted and no enclosing
environments are searched.

This is a [ primitive ](/link/primitive?package=base&version=3.6.2) function.

##  Usage

    
    
    eapply(env, FUN, …, all.names = FALSE, USE.NAMES = TRUE)

##  Arguments

env

environment to be used.

FUN

the function to be applied, found _via_ ` [ match.fun
](/link/match.fun?package=base&version=3.6.2) ` . In the case of functions
like ` + ` , ` %*% ` , etc., the function name must be backquoted or quoted.

…

optional arguments to ` FUN ` .

all.names

a logical indicating whether to apply the function to all values.

USE.NAMES

logical indicating whether the resulting list should have ` [ names
](/link/names?package=base&version=3.6.2) ` .

##  Value

A named (unless ` USE.NAMES = FALSE ` ) list. Note that the order of the
components is arbitrary for hashed environments.

##  See Also

` [ environment ](/link/environment?package=base&version=3.6.2) ` , ` [ lapply
](/link/lapply?package=base&version=3.6.2) ` .

##  Examples

[ Run this code
](https://app.datacamp.com/workspace/preview?_tag=rdocs&rdocsPath=packages%2Fbase%2Fversions%2F3.6.2%2Ftopics%2Feapply&utm_source=r-docs&utm_medium=docs&utm_term=eapply&utm_content=run_example_in_workspace)

    
    
    # NOT RUN {
    require(stats)
    
    env <- new.env(hash = FALSE) # so the order is fixed
    env$a <- 1:10
    env$beta <- exp(-3:3)
    env$logic <- c(TRUE, FALSE, FALSE, TRUE)
    # what have we there?
    utils::ls.str(env)
    
    # compute the mean for each list element
           eapply(env, mean)
    unlist(eapply(env, mean, USE.NAMES = FALSE))
    
    # median and quartiles for each element (making use of "..." passing):
    eapply(env, quantile, probs = 1:3/4)
    eapply(env, quantile)
    # }
    

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[ base  (version  3.6.2  ) ](/packages/base/versions/3.6.2)

#  writeLines: Write Lines to a Connection

##  Description

Write text lines to a connection.

##  Usage

    
    
    writeLines(text, con = stdout(), sep = "\n", useBytes = FALSE)

##  Arguments

text

A character vector

con

A [ connection ](/link/connection?package=base&version=3.6.2) object or a
character string.

sep

character string. A string to be written to the connection after each line of
text.

useBytes

logical. See ‘Details’.

##  Details

If the ` con ` is a character string, the function calls ` [ file
](/link/file?package=base&version=3.6.2) ` to obtain a file connection which
is opened for the duration of the function call.

If the connection is open it is written from its current position. If it is
not open, it is opened for the duration of the call in ` "wt" ` mode and then
closed again.

Normally ` writeLines ` is used with a text-mode connection, and the default
separator is converted to the normal separator for that platform (LF on
Unix/Linux, CRLF on Windows). For more control, open a binary connection and
specify the precise value you want written to the file in ` sep ` . For even
more control, use ` [ writeChar ](/link/writeChar?package=base&version=3.6.2)
` on a binary connection.

` useBytes ` is for expert use. Normally (when false) character strings with
marked encodings are converted to the current encoding before being passed to
the connection (which might do further re-encoding). ` useBytes = TRUE `
suppresses the re-encoding of marked strings so they are passed byte-by-byte
to the connection: this can be useful when strings have already been re-
encoded by e.g. ` [ iconv ](/link/iconv?package=base&version=3.6.2) ` . (It is
invoked automatically for strings with marked encoding ` "bytes" ` .)

##  See Also

` [ connections ](/link/connections?package=base&version=3.6.2) ` , ` [
writeChar ](/link/writeChar?package=base&version=3.6.2) ` , ` [ writeBin
](/link/writeBin?package=base&version=3.6.2) ` , ` [ readLines
](/link/readLines?package=base&version=3.6.2) ` , ` [ cat
](/link/cat?package=base&version=3.6.2) `

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[ base  (version  3.6.2  ) ](/packages/base/versions/3.6.2)

#  system.file: Find Names of R System Files

##  Description

Finds the full file names of files in packages etc.

##  Usage

    
    
    system.file(…, package = "base", lib.loc = NULL,
                mustWork = FALSE)

##  Arguments

…

character vectors, specifying subdirectory and file(s) within some package.
The default, none, returns the root of the package. Wildcards are not
supported.

package

a character string with the name of a single package. An error occurs if more
than one package name is given.

lib.loc

a character vector with path names of  R  libraries. See ‘Details’ for the
meaning of the default value of ` NULL ` .

mustWork

logical. If ` TRUE ` , an error is given if there are no matching files.

##  Value

A character vector of positive length, containing the file paths that matched
` … ` , or the empty string, ` "" ` , if none matched (unless ` mustWork =
TRUE ` ).

If matching the root of a package, there is no trailing separator.

` system.file() ` with no arguments gives the root of the  base  package.

##  Details

This checks the existence of the specified files with ` [ file.exists
](/link/file.exists?package=base&version=3.6.2) ` . So file paths are only
returned if there are sufficient permissions to establish their existence.

The unnamed arguments in ` ... ` are usually character strings, but if
character vectors they are recycled to the same length.

This uses ` [ find.package ](/link/find.package?package=base&version=3.6.2) `
to find the package, and hence with the default ` lib.loc = NULL ` looks first
for attached packages then in each library listed in ` [ .libPaths
](/link/.libPaths?package=base&version=3.6.2) () ` . Note that if a namespace
is loaded but the package is not attached, this will look only on ` [
.libPaths ](/link/.libPaths?package=base&version=3.6.2) () ` .

##  See Also

` [ R.home ](/link/R.home?package=base&version=3.6.2) ` for the root directory
of the  R  installation, ` [ list.files
](/link/list.files?package=base&version=3.6.2) ` .

` [ Sys.glob ](/link/Sys.glob?package=base&version=3.6.2) ` to find paths via
wildcards.

##  Examples

[ Run this code
](https://app.datacamp.com/workspace/preview?_tag=rdocs&rdocsPath=packages%2Fbase%2Fversions%2F3.6.2%2Ftopics%2Fsystem.file&utm_source=r-docs&utm_medium=docs&utm_term=system.file&utm_content=run_example_in_workspace)

    
    
    # NOT RUN {
    system.file()                  # The root of the 'base' package
    system.file(package = "stats") # The root of package 'stats'
    system.file("INDEX")
    system.file("help", "AnIndex", package = "splines")
    # }
    

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[ base  (version  3.6.2  ) ](/packages/base/versions/3.6.2)

#  tabulate: Tabulation for Vectors

##  Description

` tabulate ` takes the integer-valued vector ` bin ` and counts the number of
times each integer occurs in it.

##  Usage

    
    
    tabulate(bin, nbins = max(1, bin, na.rm = TRUE))

##  Arguments

bin

a numeric vector (of positive integers), or a factor. [ Long vectors
](/link/Long%20vectors?package=base&version=3.6.2) are supported.

nbins

the number of bins to be used.

##  Value

An integer valued ` [ integer ](/link/integer?package=base&version=3.6.2) ` or
` [ double ](/link/double?package=base&version=3.6.2) ` vector (without
names). There is a bin for each of the values ` 1, …, nbins ` ; values outside
that range and ` NA ` s are (silently) ignored.

On 64-bit platforms ` bin ` can have \\(2^{31}\\) or more elements (i.e., `
length(bin) > .Machine$integer.max ` ), and hence a count could exceed the
maximum integer. For this reason, the return value is of type double for such
long ` bin ` vectors.

##  Details

` tabulate ` is the workhorse for the ` [ table
](/link/table?package=base&version=3.6.2) ` function.

If ` bin ` is a factor, its internal integer representation is tabulated.

If the elements of ` bin ` are numeric but not integers, they are truncated by
` [ as.integer ](/link/as.integer?package=base&version=3.6.2) ` .

##  See Also

` [ table ](/link/table?package=base&version=3.6.2) ` , ` [ factor
](/link/factor?package=base&version=3.6.2) ` .

##  Examples

[ Run this code
](https://app.datacamp.com/workspace/preview?_tag=rdocs&rdocsPath=packages%2Fbase%2Fversions%2F3.6.2%2Ftopics%2Ftabulate&utm_source=r-docs&utm_medium=docs&utm_term=tabulate&utm_content=run_example_in_workspace)

    
    
    # NOT RUN {
    tabulate(c(2,3,5))
    tabulate(c(2,3,3,5), nbins = 10)
    tabulate(c(-2,0,2,3,3,5))  # -2 and 0 are ignored
    tabulate(c(-2,0,2,3,3,5), nbins = 3)
    tabulate(factor(letters[1:10]))
    # }
    

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[ base  (version  3.6.2  ) ](/packages/base/versions/3.6.2)

#  system.time: CPU Time Used

##  Description

Return CPU (and other) times that ` expr ` used.

##  Usage

    
    
    system.time(expr, gcFirst = TRUE)
    

##  Arguments

expr

Valid  R  expression to be timed.

gcFirst

Logical - should a garbage collection be performed immediately before the
timing? Default is ` TRUE ` .

##  Value

A object of class ` "proc_time" ` : see ` [ proc.time
](/link/proc.time?package=base&version=3.6.2) ` for details.

##  Details

` system.time ` calls the function ` [ proc.time
](/link/proc.time?package=base&version=3.6.2) ` , evaluates ` expr ` , and
then calls ` proc.time ` once more, returning the difference between the two `
proc.time ` calls.

` unix.time ` has been an alias of ` system.time ` , for compatibility with S,
and has finally been deprecated in 2016.

Timings of evaluations of the same expression can vary considerably depending
on whether the evaluation triggers a garbage collection. When ` gcFirst ` is `
TRUE ` a garbage collection ( ` [ gc ](/link/gc?package=base&version=3.6.2) `
) will be performed immediately before the evaluation of ` expr ` . This will
usually produce more consistent timings.

##  See Also

` [ proc.time ](/link/proc.time?package=base&version=3.6.2) ` , ` [ time
](/link/time?package=base&version=3.6.2) ` which is for time series.

` [ Sys.time ](/link/Sys.time?package=base&version=3.6.2) ` to get the current
date & time.

##  Examples

[ Run this code
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    # NOT RUN {
    require(stats)
    # }
    # NOT RUN {
    system.time(for(i in 1:100) mad(runif(1000)))
    # }
    # NOT RUN {
    exT <- function(n = 10000) {
      # Purpose: Test if system.time works ok;   n: loop size
      system.time(for(i in 1:n) x <- mean(rt(1000, df = 4)))
    }
    #-- Try to interrupt one of the following (using Ctrl-C / Escape):
    exT()                 #- about 4 secs on a 2.5GHz Xeon
    system.time(exT())    #~ +/- same
    # }
    

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###  [ Gtk ](index.html)

API Version: 3.0

Library Version: 3.24

#####  Type

[ Widget ](class.Widget.html)

#####  Properties

[ app-paintable ](property.Widget.app-paintable.html) [ can-default
](property.Widget.can-default.html) [ can-focus ](property.Widget.can-
focus.html) [ composite-child ](property.Widget.composite-child.html) [
double-buffered ](property.Widget.double-buffered.html) [ events
](property.Widget.events.html) [ expand ](property.Widget.expand.html) [
focus-on-click ](property.Widget.focus-on-click.html) [ halign
](property.Widget.halign.html) [ has-default ](property.Widget.has-
default.html) [ has-focus ](property.Widget.has-focus.html) [ has-tooltip
](property.Widget.has-tooltip.html) [ height-request ](property.Widget.height-
request.html) [ hexpand ](property.Widget.hexpand.html) [ hexpand-set
](property.Widget.hexpand-set.html) [ is-focus ](property.Widget.is-
focus.html) [ margin ](property.Widget.margin.html) [ margin-bottom
](property.Widget.margin-bottom.html) [ margin-end ](property.Widget.margin-
end.html) [ margin-left ](property.Widget.margin-left.html) [ margin-right
](property.Widget.margin-right.html) [ margin-start ](property.Widget.margin-
start.html) [ margin-top ](property.Widget.margin-top.html) [ name
](property.Widget.name.html) [ no-show-all ](property.Widget.no-show-all.html)
[ opacity ](property.Widget.opacity.html) [ parent
](property.Widget.parent.html) [ receives-default ](property.Widget.receives-
default.html) [ scale-factor ](property.Widget.scale-factor.html) [ sensitive
](property.Widget.sensitive.html) [ style ](property.Widget.style.html) [
tooltip-markup ](property.Widget.tooltip-markup.html) [ tooltip-text
](property.Widget.tooltip-text.html) [ valign ](property.Widget.valign.html) [
vexpand ](property.Widget.vexpand.html) [ vexpand-set
](property.Widget.vexpand-set.html) [ visible ](property.Widget.visible.html)
[ width-request ](property.Widget.width-request.html) [ window
](property.Widget.window.html)

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###  Property

#  [ Gtk ](index.html) [ Widget ](class.Widget.html) :width-request

####  Declaration

    
    
    property width-request: int [ read, write ]

####  Description

No description available.

Type: ` gint `

####  Flags

Readable  |  **yes**  
---|---  
Writable  |  **yes**  
Construct  |  **no**  
Construct only  |  **no**
![](gtk-logo.svg)

###  [ Gtk ](index.html)

API Version: 3.0

Library Version: 3.24

#####  Type

[ FileChooser ](iface.FileChooser.html)

#####  Properties

[ action ](property.FileChooser.action.html) [ create-folders
](property.FileChooser.create-folders.html) [ do-overwrite-confirmation
](property.FileChooser.do-overwrite-confirmation.html) [ extra-widget
](property.FileChooser.extra-widget.html) [ filter
](property.FileChooser.filter.html) [ local-only ](property.FileChooser.local-
only.html) [ preview-widget ](property.FileChooser.preview-widget.html) [
preview-widget-active ](property.FileChooser.preview-widget-active.html) [
select-multiple ](property.FileChooser.select-multiple.html) [ show-hidden
](property.FileChooser.show-hidden.html) [ use-preview-label
](property.FileChooser.use-preview-label.html)

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###  Property

#  [ Gtk ](index.html) [ FileChooser ](iface.FileChooser.html) :show-hidden

####  Declaration

    
    
    property show-hidden: gboolean [ read, write ]

####  Description

No description available.

Type: ` gboolean `

Getter method  |  [ ` gtk_file_chooser_get_show_hidden() ` ](method.FileChooser.get_show_hidden.html)  
---|---  
Setter method  |  [ ` gtk_file_chooser_set_show_hidden() ` ](method.FileChooser.set_show_hidden.html)  
  
####  Flags

Readable  |  **yes**  
---|---  
Writable  |  **yes**  
Construct  |  **no**  
Construct only  |  **no**