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oussama.badad
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@oussamabadad-17646
Last seen 6.1 years ago
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
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