Displaying 10 results from an estimated 10 matches for "seqlen".
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seq_len
2010 Aug 25
1
Documenting S4 Methods
I'm in the process of converting some S3 methods to S4 methods.
I have this function :
setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")})
setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) {
... ... ...
})
setMethod("enrichmentCalc", c("GenomeData", "B...
2010 Aug 30
2
S4 Method Rd Warning
...a warning in R CMD check which is seemingly not relevant to my Rd file.
The warning says :
* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'enrichmentCalc':
<unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...)
<unescaped bksl>S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, organism, seqLen=NULL, do.warn=FALSE)
<unescaped bksl>S4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism, seqLen=NULL)
Functions with \usage entries need to have the appropriate \alias entries,...
2010 Aug 30
2
S4 Method Rd Warning
...a warning in R CMD check which is seemingly not relevant to my Rd file.
The warning says :
* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'enrichmentCalc':
<unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...)
<unescaped bksl>S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, organism, seqLen=NULL, do.warn=FALSE)
<unescaped bksl>S4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism, seqLen=NULL)
Functions with \usage entries need to have the appropriate \alias entries,...
2004 Dec 30
3
labels and counting
Hello,
I have got the following problem:
given is a large string sequence consisting of the four letters "A" "C"
"G" and "T" (as before). Additionally, I have got a second string
sequence of the same length giving a label for each character. The
labels are "+" and "-".
Now I would like to create an 8x8 matrix which contains the
2007 Nov 14
1
Problem indexing text with spelling enabled in Perl
...ritableDatabase::add_spelling
(this=0xa553988, word=@0xbff97724, freqinc=1) at ./include/xapian/
base.h:154
#1 0xb7becf47 in Xapian::TermGenerator::Internal::index_text
(this=0xa553970, itor=
{p = 0xab2d69f " North Face Windwall 1 Jacket boys", end =
0xab2d6c1 "", seqlen = 1}, weight=3, prefix=@0xbff977ac,
with_positions=true)
at queryparser/termgenerator_internal.cc:207
#2 0xb7bebf0c in Xapian::TermGenerator::index_text (this=0x9b12d68,
itor=@0xbff9779c, weight=3, prefix=@0xbff977ac) at queryparser/
termgenerator.cc:90
#3 0xb7c6b6d6 in XS_Search__Xapia...
2003 May 28
0
plot() error-msg: "need finite xlim values"
...values"
---
> set.seed(123)
> state <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, + 1, 1,
1)
> markers <- c(1, 2, 1, 1, 2, 3, 3, 4, 2, 1, 1, 3, 2, 3, 2, 4, + 5, 2,
3, 4) + runif(20, -1, 1)
> roc1 <- rocdemo.sca(truth = state, data = markers, rule = dxrule.sca,
seqlen = 5)
> plot(roc1)
Error in plot.window(xlim, ylim, log, asp, ...) :
need finite xlim values
In addition: Warning messages:
1: no finite arguments to min; returning Inf
2: no finite arguments to max; returning -Inf
3: no finite arguments to min; returning Inf
4: no finite arguments to max...
2007 Dec 17
1
Crashes with spelling enabled and perl.
...uage: auto; currently c++
(gdb) bt
#0 0x001c9bbc in Xapian::WritableDatabase::add_spelling
(this=0x9d77de0, word=@0xbf846fa0, freqinc=1) at ./include/xapian/
base.h:154
#1 0x0032608a in Xapian::TermGenerator::Internal::index_text
(this=0x9d77dc8, itor={p = 0x0, end = 0x9cb5db8 "", seqlen = 0},
weight=1,
prefix=@0xbf84703c, with_positions=true) at queryparser/
termgenerator_internal.cc:207
#2 0x0032506c in Xapian::TermGenerator::index_text (this=0x9c94cd0,
itor=@0xbf84702c, weight=1, prefix=@0xbf84703c) at queryparser/
termgenerator.cc:90
#3 0x0017100e in XS_Search__Xap...
2011 Feb 17
5
[PATCH 0/4] Reduce core size
From: Matt Fleming <matt.fleming at linux.intel.com>
These patches are based on the elflink branch.
This set of patches is my attempt at moving the command-line interface
functionality out of the core and into an ELF module to reduce the
size of the core.
The most interesting patch is [PATCH 4/4] which moves the cli code out
of core/elflink and into com32/elflink/modules. [PATCH 4/4] is
2011 Mar 09
14
[PATCH 00/12] elflink shrinkage
From: Matt Fleming <matt.fleming at linux.intel.com>
This is a series of patches that,
* shrink the core by moving things into an ldlinux ELF module
* begin wiring up some of the C versions of various functions
The core now only contains essential code and loads the ldlinux module
to do everything else, like providing a command line interface and
loading kernels.
The config file parsing
2011 Apr 16
20
[PATCH 00/20] Switch to ELF modules
From: Matt Fleming <matt.fleming at linux.intel.com>
This series fixes some bugs and switches the elflink branch to be
entirely ELF modules. It applies on top of,
http://syslinux.zytor.com/archives/2011-April/016369.html
The deletions in the diff stat below are mainly from deleting
com32/elflink/modules (finally!). Now there should be no duplicate
code because we don't need COM32 and