| ... | ... |
@@ -17,7 +17,7 @@ |
| 17 | 17 |
#' |
| 18 | 18 |
#'### Obtain gene coordinates for rat from biomaRt ### |
| 19 | 19 |
#'library(biomaRt) |
| 20 |
-#'ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
|
|
| 20 |
+#'ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl') |
|
| 21 | 21 |
#'genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
|
| 22 | 22 |
#' 'end_position', 'strand', 'external_gene_name', |
| 23 | 23 |
#' 'gene_biotype'), |
| ... | ... |
@@ -24,7 +24,7 @@ |
| 24 | 24 |
#' |
| 25 | 25 |
#'## We need to get coordinates for each of the genes |
| 26 | 26 |
#'library(biomaRt) |
| 27 |
-#'ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
|
|
| 27 |
+#'ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl') |
|
| 28 | 28 |
#'genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
|
| 29 | 29 |
#' 'end_position', 'strand', 'external_gene_name', |
| 30 | 30 |
#' 'gene_biotype'), |
| ... | ... |
@@ -97,17 +97,16 @@ model <- get(load(file)) |
| 97 | 97 |
|
| 98 | 98 |
### Obtain gene coordinates for rat from biomaRt ### |
| 99 | 99 |
library(biomaRt) |
| 100 |
-ensembl <- useMart('ENSEMBL_MART_ENSEMBL', host='may2012.archive.ensembl.org',
|
|
| 101 |
- dataset='rnorvegicus_gene_ensembl') |
|
| 100 |
+ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl') |
|
| 102 | 101 |
genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
|
| 103 |
- 'end_position', 'strand', 'external_gene_id', |
|
| 102 |
+ 'end_position', 'strand', 'external_gene_name', |
|
| 104 | 103 |
'gene_biotype'), |
| 105 | 104 |
mart=ensembl) |
| 106 | 105 |
# Transform to GRanges for easier handling |
| 107 | 106 |
genes <- GRanges(seqnames=paste0('chr',genes$chromosome_name),
|
| 108 | 107 |
ranges=IRanges(start=genes$start, end=genes$end), |
| 109 | 108 |
strand=genes$strand, |
| 110 |
- name=genes$external_gene_id, biotype=genes$gene_biotype) |
|
| 109 |
+ name=genes$external_gene_name, biotype=genes$gene_biotype) |
|
| 111 | 110 |
# Rename chrMT to chrM |
| 112 | 111 |
seqlevels(genes)[seqlevels(genes)=='chrMT'] <- 'chrM' |
| 113 | 112 |
print(genes) |
| ... | ... |
@@ -33,17 +33,16 @@ head(expression_lv) |
| 33 | 33 |
|
| 34 | 34 |
## We need to get coordinates for each of the genes |
| 35 | 35 |
library(biomaRt) |
| 36 |
-ensembl <- useMart('ENSEMBL_MART_ENSEMBL', host='may2012.archive.ensembl.org',
|
|
| 37 |
- dataset='rnorvegicus_gene_ensembl') |
|
| 36 |
+ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl') |
|
| 38 | 37 |
genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
|
| 39 |
- 'end_position', 'strand', 'external_gene_id', |
|
| 38 |
+ 'end_position', 'strand', 'external_gene_name', |
|
| 40 | 39 |
'gene_biotype'), |
| 41 | 40 |
mart=ensembl) |
| 42 |
-expr <- merge(genes, expression_lv, by='ensembl_gene_id') |
|
| 41 |
+expr <- merge(genes, expression_lv, by='ensembl_gene_name') |
|
| 43 | 42 |
# Transform to GRanges |
| 44 | 43 |
expression.SHR <- GRanges(seqnames=paste0('chr',expr$chromosome_name),
|
| 45 | 44 |
ranges=IRanges(start=expr$start, end=expr$end), |
| 46 |
- strand=expr$strand, name=expr$external_gene_id, |
|
| 45 |
+ strand=expr$strand, name=expr$external_gene_name, |
|
| 47 | 46 |
biotype=expr$gene_biotype, |
| 48 | 47 |
expression=expr$expression_SHR) |
| 49 | 48 |
# We apply an asinh transformation to reduce the effect of outliers |
| ... | ... |
@@ -378,7 +378,7 @@ heatmapCountCorrelation(model) + ggtitle('Read count correlation')
|
| 378 | 378 |
# Annotations can easily be obtained with the biomaRt package. Of course, you can |
| 379 | 379 |
# also load them from file if you already have annotation files available. |
| 380 | 380 |
library(biomaRt) |
| 381 |
-ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
|
|
| 381 |
+ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl') |
|
| 382 | 382 |
genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
|
| 383 | 383 |
'end_position', 'strand', 'external_gene_name', |
| 384 | 384 |
'gene_biotype'), |
| ... | ... |
@@ -436,7 +436,7 @@ head(expression_lv) |
| 436 | 436 |
|
| 437 | 437 |
# We need to get coordinates for each of the genes |
| 438 | 438 |
library(biomaRt) |
| 439 |
-ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
|
|
| 439 |
+ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl') |
|
| 440 | 440 |
genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
|
| 441 | 441 |
'end_position', 'strand', 'external_gene_name', |
| 442 | 442 |
'gene_biotype'), |
| ... | ... |
@@ -537,7 +537,7 @@ print(model$frequencies) |
| 537 | 537 |
# Annotations can easily be obtained with the biomaRt package. Of course, you can |
| 538 | 538 |
# also load them from file if you already have annotation files available. |
| 539 | 539 |
library(biomaRt) |
| 540 |
-ensembl <- useMart('ensembl', dataset='rnorvegicus_gene_ensembl')
|
|
| 540 |
+ensembl <- useEnsembl(biomart='ENSEMBL_MART_ENSEMBL', dataset='rnorvegicus_gene_ensembl') |
|
| 541 | 541 |
genes <- getBM(attributes=c('ensembl_gene_id', 'chromosome_name', 'start_position',
|
| 542 | 542 |
'end_position', 'strand', 'external_gene_name', |
| 543 | 543 |
'gene_biotype'), |
