1. chromstaR
  2. Commit d60467a9b26d0df5e959a76e6f51d830b187fbf6
Browse code

fixed ensembl host issue

ataudt authored on 29/10/2021 07:35:49
Showing 3 changed files
R/enrichmentAnalysis.R
History View file @ d60467a
... ... 
@@ -17,17 +17,16 @@
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 #'
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 #'### Obtain gene coordinates for rat from biomaRt ###
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 #'library(biomaRt)
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-#'ensembl <- useMart('ENSEMBL_MART_ENSEMBL', host='may2012.archive.ensembl.org',
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-#'                   dataset='rnorvegicus_gene_ensembl')
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+#'ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
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 #'genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
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-#'                            'end_position', 'strand', 'external_gene_id',
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+#'                            'end_position', 'strand', 'external_gene_name',
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 #'                            'gene_biotype'),
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 #'               mart=ensembl)
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 #'# Transform to GRanges for easier handling
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 #'genes <- GRanges(seqnames=paste0('chr',genes$chromosome_name),
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 #'                 ranges=IRanges(start=genes$start, end=genes$end),
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 #'                 strand=genes$strand,
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-#'                 name=genes$external_gene_id, biotype=genes$gene_biotype)
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+#'                 name=genes$external_gene_name, biotype=genes$gene_biotype)
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 #'# Rename chrMT to chrM
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 #'seqlevels(genes)[seqlevels(genes)=='chrMT'] <- 'chrM'
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 #'print(genes)
R/expressionAnalysis.R
History View file @ d60467a
... ... 
@@ -24,17 +24,16 @@
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 #'
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 #'## We need to get coordinates for each of the genes
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 #'library(biomaRt)
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-#'ensembl <- useMart('ENSEMBL_MART_ENSEMBL', host='may2012.archive.ensembl.org',
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-#'                   dataset='rnorvegicus_gene_ensembl')
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+#'ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
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 #'genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
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-#'                            'end_position', 'strand', 'external_gene_id',
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+#'                            'end_position', 'strand', 'external_gene_name',
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 #'                            'gene_biotype'),
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 #'               mart=ensembl)
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-#'expr <- merge(genes, expression_lv, by='ensembl_gene_id')
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+#'expr <- merge(genes, expression_lv, by='ensembl_gene_name')
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 #'# Transform to GRanges
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 #'expression.SHR <- GRanges(seqnames=paste0('chr',expr$chromosome_name),
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 #'                          ranges=IRanges(start=expr$start, end=expr$end),
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-#'                          strand=expr$strand, name=expr$external_gene_id,
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+#'                          strand=expr$strand, name=expr$external_gene_name,
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 #'                          biotype=expr$gene_biotype,
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 #'                          expression=expr$expression_SHR)
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 #'# We apply an asinh transformation to reduce the effect of outliers
vignettes/chromstaR.Rnw
History View file @ d60467a
... ... 
@@ -378,17 +378,16 @@ heatmapCountCorrelation(model) + ggtitle('Read count correlation')
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 # Annotations can easily be obtained with the biomaRt package. Of course, you can
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 # also load them from file if you already have annotation files available.
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 library(biomaRt)
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-ensembl <- useMart('ENSEMBL_MART_ENSEMBL', host='may2012.archive.ensembl.org',
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-                   dataset='rnorvegicus_gene_ensembl')
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+ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
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 genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
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-                            'end_position', 'strand', 'external_gene_id',
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+                            'end_position', 'strand', 'external_gene_name',
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                             'gene_biotype'),
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                mart=ensembl)
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 # Transform to GRanges for easier handling
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 genes <- GRanges(seqnames=paste0('chr',genes$chromosome_name),
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                  ranges=IRanges(start=genes$start, end=genes$end),
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                  strand=genes$strand,
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-                 name=genes$external_gene_id, biotype=genes$gene_biotype)
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+                 name=genes$external_gene_name, biotype=genes$gene_biotype)
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 # Rename chrMT to chrM to avoid warnings
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 seqlevels(genes)[seqlevels(genes)=='chrMT'] <- 'chrM'
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 # Select only chr12 to avoid warnings
... ... 
@@ -437,17 +436,16 @@ head(expression_lv)
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 # We need to get coordinates for each of the genes
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 library(biomaRt)
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-ensembl <- useMart('ENSEMBL_MART_ENSEMBL', host='may2012.archive.ensembl.org',
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-                   dataset='rnorvegicus_gene_ensembl')
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+ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
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 genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
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-                            'end_position', 'strand', 'external_gene_id',
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+                            'end_position', 'strand', 'external_gene_name',
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                             'gene_biotype'),
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                mart=ensembl)
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-expr <- merge(genes, expression_lv, by='ensembl_gene_id')
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+expr <- merge(genes, expression_lv, by='ensembl_gene_name')
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 # Transform to GRanges
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 expression.SHR <- GRanges(seqnames=paste0('chr',expr$chromosome_name),
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                           ranges=IRanges(start=expr$start, end=expr$end),
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-                          strand=expr$strand, name=expr$external_gene_id,
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+                          strand=expr$strand, name=expr$external_gene_name,
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                           biotype=expr$gene_biotype,
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                           expression=expr$expression_SHR)
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 # Rename chrMT to chrM to avoid warnings
... ... 
@@ -539,17 +537,16 @@ print(model$frequencies)
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 # Annotations can easily be obtained with the biomaRt package. Of course, you can
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 # also load them from file if you already have annotation files available.
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 library(biomaRt)
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-ensembl <- useMart('ENSEMBL_MART_ENSEMBL', host='may2012.archive.ensembl.org',
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-                   dataset='rnorvegicus_gene_ensembl')
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+ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
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 genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
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-                            'end_position', 'strand', 'external_gene_id',
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+                            'end_position', 'strand', 'external_gene_name',
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                             'gene_biotype'),
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                mart=ensembl)
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 # Transform to GRanges for easier handling
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 genes <- GRanges(seqnames=paste0('chr',genes$chromosome_name),
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                  ranges=IRanges(start=genes$start, end=genes$end),
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                  strand=genes$strand,
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-                 name=genes$external_gene_id, biotype=genes$gene_biotype)
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+                 name=genes$external_gene_name, biotype=genes$gene_biotype)
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 # Rename chrMT to chrM to avoid warnings
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 seqlevels(genes)[seqlevels(genes)=='chrMT'] <- 'chrM'
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 # Select only chr12 to avoid warnings