MEDIP: Problem with MEDIPS.createSet
1
1
Entering edit mode
vjain • 0
@vjain-15283
Last seen 6.7 years ago
hESCs_MeDIP = MEDIPS.createSet(file = reads1, BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq, window_size = ws)
Error in strsplit(file, "/") : non-character argument

I uploaded my bam file named "reads1" using readGAlignments in R.

Later I come across this error. I even edited my .BAM file according to BSgenome. I am unable to figure out the error. 

Please help.
medips bsgenome medip-seq • 2.2k views
ADD COMMENT •
0
Entering edit mode
Lukas Chavez ▴ 570
@lukas-chavez-5781
Last seen 6.8 years ago
USA/La Jolla/UCSD
Hi Vjain, MEDIPS expects a bam file like file=“/path/to/file.bam”. Please do not specify a preprocessed bam file object. All the best, Lukas On Mar 19, 2018, at 2:27 AM, vjain [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User vjain<https: support.bioconductor.org="" u="" 15283=""/> wrote Question: MEDIP: Problem with MEDIPS.createSet<https: support.bioconductor.org="" p="" 107126=""/>: hESCs_MeDIP = MEDIPS.createSet(file = reads1, BSgenome = BSgenome, extend = extend, shift = shift, uniq = uniq, window_size = ws) Error in strsplit(file, "/") : non-character argument ________________________________ I uploaded my bam file named "reads1" using readGAlignments in R. Later I come across this error. I even edited my .BAM file according to BSgenome. I am unable to figure out the error. Please help. ________________________________ Post tags: medips, bsgenome, medip-seq You may reply via email or visit MEDIP: Problem with MEDIPS.createSet
ADD COMMENT •
0
Entering edit mode

Hi Lukas

I tried giving the path and got the following error:

Error in as.environment(pos) : 
  no item called "paste("package:", BSgenome, sep = "")" on the search list
In addition: Warning message:
In ls(paste("package:", BSgenome, sep = "")) :
  ‘paste("package:", BSgenome, sep = "")’ converted to character string
ADD REPLY •
0
Entering edit mode

Hi Lucas I figured out the error,

the next problem arising is the following:

CS = MEDIPS.couplingVector(pattern = "CG", refObj = Set1[[1]])
Error in Set1[[1]] : this S4 class is not subsettable

please help.

Thank You

ADD REPLY •
0
Entering edit mode
Hi Vjain, Would you please share your solution to your error? For the new error: it seems as if you try to access a subset of Set1 by Set1[[1]] even though there are no subsets. Have you simply tried refObj = Set1 ? Best, Lukas On Mar 20, 2018, at 2:51 AM, vjain [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User vjain<https: support.bioconductor.org="" u="" 15283=""/> wrote Comment: MEDIP: Problem with MEDIPS.createSet<https: support.bioconductor.org="" p="" 107126="" #107158="">: Hi Lucas I figured out the error, the next problem arising is the following: CS = MEDIPS.couplingVector(pattern = "CG", refObj = Set1[[1]]) Error in Set1[[1]] : this S4 class is not subsettable please help. Thank You ________________________________ Post tags: medips, bsgenome, medip-seq You may reply via email or visit C: MEDIP: Problem with MEDIPS.createSet
ADD REPLY •
0
Entering edit mode

Hi Lucas, 

Solution to my previous error was just that I wrote :

BSgenome = BSgenome.Sscrofa.UCSC.susScr3 

instead of BSgenome = "BSgenome.Sscrofa.UCSC.susScr3"

 

Also, I am facing a new issue in MEDIPS.saturation, i.e.

 sr = MEDIPS.saturation(file = "/home/mobashirm/PRJ2017Nov2017/drmohan/MEDIP/test_chr.bam", BSgenome = BSgenome,uniq = uniq, extend = extend, shift = shift, window_size = ws, nit = 10, nrit = 1, empty_bins = TRUE,rank = FALSE)
Reading bam alignment test_chr.bam 
Total number of imported short reads: 58473177
Extending reads...
Creating GRange Object...
Keep at most NaN read(s) mapping to the same genomic location
Number of remaining reads: 58473177
Loading chromosome lengths for BSgenome.Sscrofa.UCSC.susScr3...
Calculating genomic coordinates...Error in vector(length = supersize_chr[length(chromosomes)], mode = "character") : 
  vector size cannot be NA/NaN
In addition: Warning message:
In qpois(1 - as.numeric(uniq), length(regions_GRange)/sum(as.numeric(seqlengths(dataset)[chr.select]))) :
  NaNs produced

 

Can you please help me with this too.

Thank You

ADD REPLY •
0
Entering edit mode
Hi Vjain, The chromosome names of your custom genome might not match the chromosome names of your sequencing reads? See for example this previous question: MEDIPS.createSet error Lukas On Mar 21, 2018, at 3:33 AM, vjain [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User vjain<https: support.bioconductor.org="" u="" 15283=""/> wrote Comment: MEDIP: Problem with MEDIPS.createSet<https: support.bioconductor.org="" p="" 107126="" #107223="">: Hi Lucas, Solution to my previous error was just that I wrote : BSgenome = BSgenome.Sscrofa.UCSC.susScr3 instead of BSgenome = "BSgenome.Sscrofa.UCSC.susScr3" Also, I am facing a new issue in MEDIPS.saturation, i.e. sr = MEDIPS.saturation(file = "/home/mobashirm/PRJ2017Nov2017/drmohan/MEDIP/test_chr.bam", BSgenome = BSgenome,uniq = uniq, extend = extend, shift = shift, window_size = ws, nit = 10, nrit = 1, empty_bins = TRUE,rank = FALSE) Reading bam alignment test_chr.bam Total number of imported short reads: 58473177 Extending reads... Creating GRange Object... Keep at most NaN read(s) mapping to the same genomic location Number of remaining reads: 58473177 Loading chromosome lengths for BSgenome.Sscrofa.UCSC.susScr3... Calculating genomic coordinates...Error in vector(length = supersize_chr[length(chromosomes)], mode = "character") : vector size cannot be NA/NaN In addition: Warning message: In qpois(1 - as.numeric(uniq), length(regions_GRange)/sum(as.numeric(seqlengths(dataset)[chr.select]))) : NaNs produced Can you please help me with this too. Thank You ________________________________ Post tags: medips, bsgenome, medip-seq You may reply via email or visit C: MEDIP: Problem with MEDIPS.createSet
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 399 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6