greenleaflab/chromvarmotifs

R package with motifs for use with chromVAR

chromvarmotifs's Issues

PWMatrix list from local transfac file

Dear Team ChromVAR,

Your tools have been wonderful for our research. I’m wondering if there is any tool I can use to construct a PWMatrix list from a local transfac motif file with counts in the matrix.

Thanks in advance,
Y.

script for converting homer motifs

Only a subset of homer motifs is available in this package (332 out of 436). I would highly appreciate it if the script used to convert homer motifs into PWM could be disclosed. Thanks!!!

curation process for the cisBP data

Hello
I would like to know details on the curation process for the PWMs provided in the human_pwms_v1 dataset.
Many thanks
-Burak

Which version of cisBP pwm to use with chromVAR?

Thank you for writing a great piece of software and adding in the cisBP data! A quick question, which version should be used with chromVAR? v1 or v2?

Thanks!

Installation error

HI

When I installed it on my linux server, I received an error message: No methods found in package'IRanges' for request:'score' when loading'TFBSTools'.

How to solve it?

pwms data file link does not exist issue

Tried to install the package following the instruction. It gave several Rd warnings. Please see detail logs below. The result is that all the pwms data are empty when I try to load with data().
Could you find a permanent solutions to this bug other than manually loading them each time in order to use it?
(R studio with R3.5.2 on windows 10)
Thank you!
Z.

---

library(devtools)
devtools::install_github("GreenleafLab/chromVARmotifs")
Downloading GitHub repo GreenleafLab/chromVARmotifs@master
These packages have more recent versions available.
Which would you like to update?

1: VGAM (1.0-6 -> 1.1-1) [CRAN]

Enter one or more numbers separated by spaces, or an empty line to cancel
1: 1
VGAM (1.0-6 -> 1.1-1) [CRAN]
Installing 1 packages: VGAM
Installing package into ‘C:/Rpackages/3.5’
(as ‘lib’ is unspecified)

There is a binary version available but the source version is later:
binary source needs_compilation
VGAM 1.0-6 1.1-1 TRUE

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/VGAM_1.0-6.zip'
Content type 'application/zip' length 7789645 bytes (7.4 MB)
downloaded 7.4 MB

package ‘VGAM’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\mzhib\AppData\Local\Temp\RtmpK4IkZ8\downloaded_packages
√ checking for file 'C:\Users\mzhib\AppData\Local\Temp\RtmpK4IkZ8\remotes39dc69e9327c\GreenleafLab-chromVARmotifs-38bed55/DESCRIPTION' (448ms)

• preparing 'chromVARmotifs':
  √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• looking to see if a 'data/datalist' file should be added
• building 'chromVARmotifs_0.2.0.tar.gz' (672ms)
  Installing package into ‘C:/Rpackages/3.5’
  (as ‘lib’ is unspecified)

• installing source package 'chromVARmotifs' ...
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  converting help for package 'chromVARmotifs'
  finding HTML links ... done
  chromVARmotifs html
  encode_pwms html
  Rd warning: C:/Users/mzhib/AppData/Local/Temp/RtmpQBR36E/R.INSTALL78850623c46/chromVARmotifs/man/encode_pwms.Rd:11: file link 'XMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  homer_pwms html
  Rd warning: C:/Users/mzhib/AppData/Local/Temp/RtmpQBR36E/R.INSTALL78850623c46/chromVARmotifs/man/homer_pwms.Rd:11: file link 'XMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  human_pwms_v1 html
  Rd warning: C:/Users/mzhib/AppData/Local/Temp/RtmpQBR36E/R.INSTALL78850623c46/chromVARmotifs/man/human_pwms_v1.Rd:11: file link 'XMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  human_pwms_v2 html
  Rd warning: C:/Users/mzhib/AppData/Local/Temp/RtmpQBR36E/R.INSTALL78850623c46/chromVARmotifs/man/human_pwms_v2.Rd:11: file link 'XMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  mouse_pwms_v1 html
  Rd warning: C:/Users/mzhib/AppData/Local/Temp/RtmpQBR36E/R.INSTALL78850623c46/chromVARmotifs/man/mouse_pwms_v1.Rd:11: file link 'XMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  mouse_pwms_v2 html
  Rd warning: C:/Users/mzhib/AppData/Local/Temp/RtmpQBR36E/R.INSTALL78850623c46/chromVARmotifs/man/mouse_pwms_v2.Rd:11: file link 'XMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  ** building package indices
  ** testing if installed package can be loaded
• DONE (chromVARmotifs)
  In R CMD INSTALL

pooling pwmatrices together

With the exception of added redundancies and computational time for motif_ix, is there anything wrong with doing this?

library(BSgenome.Hsapiens.UCSC.hg18)
library(chromVARmotifs)
library(TFBSTools)
data("homer_pwms")
data("encode_pwms")
data("human_pwms_v2")
motifs<-do.call(PWMatrixList,c(encode_pwms,homer_pwms,human_pwms_v1))