Comments (8)
I will look into this. See #14 -- Are you using a custom database? Is it cached?
Maybe the database isn't correctly going through readBed
.
from lola.
Yes, I am using a custom database. Since I am getting this warning I don't think the database is cached:
You don't have simpleCache installed, so you won't be able to cache the
regionDB after reading it in. Install simpleCache to speed up later database
loading.
from lola.
I cannot reproduce this error. Make sure you're using the latest version of LOLA ( install with devtools::install_github("nsheff/LOLA")
.
If you can produce a reproducible example, I can look at it again.
In this example:
dbPath = system.file("extdata", "hg19", package="LOLA")
regionDB = loadRegionDB(dbLocation=dbPath)
The database in R looks like:
1 chr1 [ 28736, 29810] *
2 chr1 [135125, 135563] *
3 chr1 [327791, 328229] *
while the file looks like:
chr1 28735 29810
chr1 135124 135563
chr1 327790 328229
So, it is in fact correctly adding 1 to the left coordinate. If your version of LOLA is not adding 1 to the left side, make sure you're using the latest version.
EDIT: fix example code
from lola.
Hi Nathan,
Could you please try these lines of code for me:
library(LOLA)
dbPath <- "fakeDatabase"
regionDB <- loadRegionDB(dbPath)
regionDB
with the attached fakeDatabase? I think I am using the latest version, so I don't understand it.
The file is:
scaffold_19 23641645 23642149
scaffold_13 24500587 24501311
scaffold_0 23378037 23378626
...
And in R it looks like:
seqnames ranges strand
<Rle> <IRanges> <Rle>
1 scaffold_19 [23641645, 23642149] *
2 scaffold_13 [24500587, 24501311] *
3 scaffold_0 [23378037, 23378626] *
Thanks, Katrin
from lola.
Hi Katrin, what does your sessionInfo
say? You're likely not using the latest version. With your database, I get:
seqnames ranges strand
<Rle> <IRanges> <Rle>
1 scaffold_19 [23641646, 23642149] *
2 scaffold_13 [24500588, 24501311] *
3 scaffold_0 [23378038, 23378626] *
from lola.
This is my sessionInfo
:
> sessionInfo("LOLA")
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
locale:
[1] C
attached base packages:
character(0)
other attached packages:
[1] LOLA_1.5.0
loaded via a namespace (and not attached):
[1] zlibbioc_1.18.0 IRanges_2.6.1 graphics_3.3.1
[4] XVector_0.12.1 parallel_3.3.1 GenomicRanges_1.24.3
[7] utils_3.3.1 grDevices_3.3.1 stats_3.3.1
[10] datasets_3.3.1 S4Vectors_0.10.3 data.table_1.9.6
[13] methods_3.3.1 BiocGenerics_0.18.0 chron_2.3-47
[16] GenomeInfoDb_1.8.7 stats4_3.3.1 base_3.3.1
from lola.
you're using the LOLA version from bioconductor. the correction is on github and hasn't been put in bioc yet.
please see my previous comment.
I cannot reproduce this error. Make sure you're using the latest version of LOLA ( install with devtools::install_github("nsheff/LOLA").
from lola.
Thank you, it is working now.
from lola.
Related Issues (20)
- hg38 database HOT 1
- Add in missing cellType/antibody entries for encodeTFBSmm10 HOT 6
- Re-order result columns
- Different results between LOLAweb interactive server and local R package HOT 7
- Inclusion of mm10 JASAPR prediction track into LOLA JASPAR HOT 3
- cistrome_mm10 HOT 2
- runLOLA results table for PEP databases
- PEP file read caching HOT 2
- Can't load an example regionDB. HOT 3
- PEP tag system
- testing for enrichment of significant individual cpgs HOT 2
- Error if GRangesList has names HOT 2
- question: how to test two region sets for differential enrichment with buildRestrictedUniverse? HOT 2
- Each of the 2 combined objects has sequence levels not in the other: HOT 4
- R package error HOT 4
- LOLA runLOLA-regionDB to use for tissue-specific TFBS
- P4 tool not grouping according to the paper!!
- Error by using extractEnrichmentOverlap function
- Fisher test - two sided hypothesis
- Error when trying to load a regionDB
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from lola.