Question

MEDIP: Problem with MEDIPS.createSet

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vjain • 0

@vjain-15283

Last seen 6.6 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 • link updated 6.7 years ago by Lukas Chavez ▴ 570 • written 6.7 years ago by vjain • 0

score 0 · Answer 1 · 2018-03-19

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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 • link 6.7 years ago Lukas Chavez ▴ 570

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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 • link 6.7 years ago vjain • 0

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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 • link 6.7 years ago vjain • 0

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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 • link 6.7 years ago Lukas Chavez ▴ 570

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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 • link 6.7 years ago vjain • 0

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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 • link 6.7 years ago Lukas Chavez ▴ 570