wzthu/enrichtf

Bioconductor package enrichTF: Transcription Factors Enrichment Analysis

enrichtf's Issues

error configuring motifpwm

Hi,
I am working my way through the vignette and encountered the following error:

PECA_TF_enrich(inputForegroundBed = '/Users/malinjl/Desktop/ATAC-Seq_data/test.bed', genome = "mm10")
Configure bsgenome ...
Configure bsgenome finished
Configure motifpwm ...
trying URL 'https://wzthu.github.io/enrich/refdata/mm10/all_motif_rmdup.gz'
Error in download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath, :
cannot open URL 'https://wzthu.github.io/enrich/refdata/mm10/all_motif_rmdup.gz'
In addition: Warning message:
In download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath, :
cannot open URL 'https://wzthu.github.io/enrich/refdata/mm10/all_motif_rmdup.gz': HTTP status was '404 Not Found'

Could you please provide a workaround for this error?

Thanks,
Justin

error for hg19 Genome

I got an error when using —— setGenome("hg19") ：
Configure bsgenome ...
Configure bsgenome finished
Configure motifpwm ...
Configure motifpwm finished
Configure motifPWMOBJ ...
Configure motifPWMOBJ finished
Configure RE_gene_corr ...
Configure RE_gene_corr finished
Configure Enhancer_RE_gene_corr ...
Configure Enhancer_RE_gene_corr finished
Configure MotifTFTable ...
Configure MotifTFTable finished
Configure MotifWeights ...
Configure MotifWeights finished
Configure TFgeneRelMtx ...
Configure TFgeneRelMtx finished
Configure SampleName ...
Configure SampleName finished
Configure OpenRegion ...
Configure OpenRegion finished
Configure ConserveRegion ...
Configure ConserveRegion finished
Configure HOMER ...
Error in runWithFinishCheck(func = checkAndInstallHOMER, "HOMER", refFilePath = "HOMER") :
file.exists(refFilePath) is not TRUE
Any suggestions?

R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

How to give custom set of background region

Hi Authors!!

I am looking forward to using enrichTF package for a set of ~1000 enhancer regions that I have for putative TF enrichment analysis.

I have a custom set of background regions (for each enhancer I have 4 randomly sampled regions with similar GC content and same length i.e. 1000 bp). How can I use this custom set of background regions? Is it necessary that the number of regions in our positive set must be equal to the number of regions in the negative set as well?

EDIT 1

Also the regions in test dataset have start coordinate 2bp more than the regions available in the testregion.foreground.bed

[1]     chr1   1690154-1691153      *
  [2]     chr1   1784734-1785733      *
  [3]     chr1   9797247-9798246      *
  [4]     chr1   9828095-9829094      *
  [5]     chr1 12203230-12204229      *
  [6]     chr1 15063575-15064574      *
  [7]     chr1 15266160-15267159      *
  [8]     chr1 15294621-15295620      *
  [9]     chr1 15406202-15407201      *

chr1	1690152	1691153	1	0	.
chr1	1784732	1785733	2	0	.
chr1	9797245	9798246	3	0	.
chr1	9828093	9829094	4	0	.
chr1	12203228	12204229	5	0	.
chr1	15063573	15064574	6	0	.
chr1	15266158	15267159	7	0	.
chr1	15294619	15295620	8	0	.
chr1	15406200	15407201	9	0	.

What's the reason behind this and how it can be prevented?

EDIT 2

I also observed that the background set generated is usually from one chromosome which is not the way we want our background to be. I therefore edited the background.bed all.bed file by randomly sampling 1000 random region from the 4000 background region set that we produced. However when we run the enrichFindMotifsInRegions function, I get the following error

>>>>>>==========================================================
Step Name:pipe_FindMotifsInRegions
All Parameters for This Step:
|Input:
|    inputRegionBed:
|        "F:\processed\final_data\ccRes\hsap_hg38_loc_nfr\enrichTF-pipeline/Step_00_pipe_GenBackground/combined_end_newcoor.txt.allregion.bed"
|Output:
|    outputRegionMotifBed:
|        "F:\processed\final_data\ccRes\hsap_hg38_loc_nfr\enrichTF-pipeline/Step_02_pipe_FindMotifsInRegions/combined_end_newcoor.txt.region.motif.bed"
|    outputMotifBed:
|        "F:\processed\final_data\ccRes\hsap_hg38_loc_nfr\enrichTF-pipeline/Step_02_pipe_FindMotifsInRegions/combined_end_newcoor.txt.motif.bed"
|Other Parameters:
|    motifRc:
|        "integrate"
|    pwmObj:
|        An object of PWMatrixList
|    genome:
|        "hg19"
|    threads:
|        2
__________________________________________
Begin to check if it is finished...
2021-01-05 22:07:26
New step. Start processing data: 
Error in checkForRemoteErrors(val) : 
  2 nodes produced errors; first error: trying to load regions beyond the boundaries of non-circular sequence "chr17"

I realised that the testgenome is not complete genome (that too hg19 not 38) and I tried using hg38. However I get the following error

Configure motifpwm ...
trying URL 'https://wzthu.github.io/enrich/refdata/hg38/all_motif_rmdup.gz'
Error in download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath,  : 
  cannot open URL 'https://wzthu.github.io/enrich/refdata/hg38/all_motif_rmdup.gz'
In addition: Warning message:
In download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath,  :
  cannot open URL 'https://wzthu.github.io/enrich/refdata/hg38/all_motif_rmdup.gz': HTTP status was '404 Not Found'

Kindly help

hg38 genome not working

It is trying to download information from an inexistent website (https://wzthu.github.io/**enrich**)

trying URL 'https://wzthu.github.io/enrich/refdata/hg38/all_motif_rmdup.gz'
Error in download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath, :
cannot open URL 'https://wzthu.github.io/enrich/refdata/hg38/all_motif_rmdup.gz'
In addition: Warning message:
In download.file(url = sprintf(urlplaceholder, genome), destfile = paste0(refFilePath, :
cannot open URL 'https://wzthu.github.io/enrich/refdata/hg38/all_motif_rmdup.gz': HTTP status was '404 Not Found'

error for enrichtf

Hi! I have another error!

`result <- enrichTFsEnrichInRegions(gen) # test whether each TF is enriched on input regions.

==========================================================
Error in FUN(X[[i]], ...) :
There is not any finish step like FindMotifsInRegions in this pipeline`

`sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.54.0
[3] rtracklayer_1.46.0 Biostrings_2.54.0
[5] XVector_0.26.0 GenomicRanges_1.38.0
[7] GenomeInfoDb_1.22.1 IRanges_2.20.2
[9] S4Vectors_0.24.4 BiocGenerics_0.32.0
[11] magrittr_1.5 enrichTF_1.2.3
[13] pipeFrame_1.2.2
`