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Question: create.set on MEDIPS
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gravatar for oussama.badad
26 days ago by
oussama.badad0 wrote:

Hi

i am tying to import my bam files for MEDIP-seq analysis, using a custom BSgenome .

my bam files are in "MEDIPS_BAMs" directory

i am using the following command :

> AKM-ANF_MeDIP = MEDIPS.createSet(file = "MEDIPS_BAMs/AKM-ANF.sorted.bam", BSgenome = BSgenome.Oeuropaea.IOGC.v1, extend = 300, shift = 0, uniq = TRUE, window_size = 100).

i get the following error message:

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

your help is very appreciated .

oussama

ADD COMMENTlink modified 26 days ago by Lukas Chavez480 • written 26 days ago by oussama.badad0
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gravatar for Lukas Chavez
26 days ago by
Lukas Chavez480
USA/La Jolla/UCSD
Lukas Chavez480 wrote:
Hi Oussama, Have you successfully loaded the BSgenome such as library(BSgenome.Oeuropaea.IOGC.v1)? Best, Lukas On Nov 14, 2018, at 3:29 PM, oussama.badad [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 oussama.badad<https: support.bioconductor.org="" u="" 17646=""/> wrote Question: create.set on MEDIPS<https: support.bioconductor.org="" p="" 115123=""/>: Hi i am tying to import my bam files for MEDIP-seq analysis, using a custom BSgenome . my bam files are in "MEDIPS_BAMs" directory i am using the following command : > AKM-ANF_MeDIP = MEDIPS.createSet(file = "MEDIPS_BAMs/AKM-ANF.sorted.bam", BSgenome = BSgenome.Oeuropaea.IOGC.v1, extend = 300, shift = 0, uniq = TRUE, window_size = 100). i get the following error message: 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 your help is very appreciated . oussama ________________________________ Post tags: medips, createset You may reply via email or visit create.set on MEDIPS
ADD COMMENTlink written 26 days ago by Lukas Chavez480

Hi Lukas

yes indeed , first i installed the BSgenome

R CMD INSTALL BSgenome.Oeuropaea.IOGC.v1_1.0.tar.gz
* installing to library ‘/scratch/obadad/anaconda3/envs/medip/lib/R/library’
* installing *source* package ‘BSgenome.Oeuropaea.IOGC.v1’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BSgenome.Oeuropaea.IOGC.v1)


then  i opened R in my console and called the MEDIPS package

> library(MEDIPS)
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: rtracklayer
Loading required package: Rsamtools

then i called the

> library(BSgenome.Oeuropaea.IOGC.v1) no error it just gives me the hand to continue

>

if i use the  available.genomes() am i supposed to see my BSgenome in the list ? because its not !!

thanks

oussama

ADD REPLYlink written 26 days ago by oussama.badad0
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