Fix the case of unavailable UCSC website
Ge Tan authored on 01/11/2018 18:42:17
| ... | ... |
@@ -59,6 +59,8 @@ |
| 59 | 59 |
} |
| 60 | 60 |
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| 61 | 61 |
\examples{
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| 62 |
+ library(BSgenome.Drerio.UCSC.danRer10) |
|
| 63 |
+ library(BSgenome.Hsapiens.UCSC.hg38) |
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| 62 | 64 |
axtFnHg38DanRer10 <- file.path(system.file("extdata", package="CNEr"),
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| 63 | 65 |
"hg38.danRer10.net.axt") |
| 64 | 66 |
axtHg38DanRer10 <- readAxt(axtFnHg38DanRer10) |
| ... | ... |
@@ -71,8 +73,8 @@ |
| 71 | 73 |
bedDanRer10Fn <- file.path(system.file("extdata", package="CNEr"),
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| 72 | 74 |
"filter_regions.danRer10.bed") |
| 73 | 75 |
bedDanRer10 <- readBed(bedDanRer10Fn) |
| 74 |
- qSizesHg38 <- fetchChromSizes("hg38")
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|
| 75 |
- qSizesDanRer10 <- fetchChromSizes("danRer10")
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|
| 76 |
+ qSizesHg38 <- seqinfo(BSgenome.Hsapiens.UCSC.hg38) |
|
| 77 |
+ qSizesDanRer10 <- seqinfo(BSgenome.Drerio.UCSC.danRer10) |
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| 76 | 78 |
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| 77 | 79 |
## Axt object |
| 78 | 80 |
windows <- c(50L, 50L, 50L) |
| ... | ... |
@@ -1,27 +1,27 @@ |
| 1 | 1 |
\name{fetchChromSizes}
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| 2 | 2 |
\alias{fetchChromSizes}
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| 3 | 3 |
\title{
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| 4 |
-fetchChromSizes function. |
|
| 4 |
+ fetchChromSizes function. |
|
| 5 | 5 |
} |
| 6 | 6 |
\description{
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| 7 |
-This function tries to automate the fetch of chromosome sizes for assemblies |
|
| 7 |
+ This function tries to automate the fetch of chromosome sizes for assemblies |
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| 8 | 8 |
from UCSC. |
| 9 | 9 |
} |
| 10 | 10 |
\usage{
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| 11 |
-fetchChromSizes(assembly) |
|
| 12 |
- |
|
| 11 |
+ fetchChromSizes(assembly) |
|
| 13 | 12 |
} |
| 14 | 13 |
\arguments{
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| 15 | 14 |
\item{assembly}{
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| 16 | 15 |
A \code{character} object: the canonical name of assembly,
|
| 17 |
- i.e., hg19 for UCSC. |
|
| 16 |
+ i.e., \sQuote{hg19} for UCSC.
|
|
| 18 | 17 |
} |
| 19 | 18 |
} |
| 20 | 19 |
\details{
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| 21 |
-This function utilises mysql queries for UCSC assemblies. |
|
| 20 |
+ This function downloads \sQuote{chromInfo.txt.gz} from UCSC golden path
|
|
| 21 |
+ for UCSC assemblies. |
|
| 22 | 22 |
} |
| 23 | 23 |
\value{
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| 24 |
-A object of \code{Seqinfo} is returned.
|
|
| 24 |
+ A object of \code{Seqinfo} is returned.
|
|
| 25 | 25 |
} |
| 26 | 26 |
\author{
|
| 27 | 27 |
Ge Tan |
| ... | ... |
@@ -30,7 +30,6 @@ A object of \code{Seqinfo} is returned.
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| 30 | 30 |
Currently, the assemblies from UCSC are supported. |
| 31 | 31 |
} |
| 32 | 32 |
|
| 33 |
- |
|
| 34 | 33 |
\examples{
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| 35 | 34 |
\donttest{
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| 36 | 35 |
fetchChromSizes("hg19")
|
| ... | ... |
@@ -61,13 +61,14 @@ |
| 61 | 61 |
} |
| 62 | 62 |
\examples{
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| 63 | 63 |
library(GenomeInfoDb) |
| 64 |
- |
|
| 64 |
+ library(BSgenome.Ggallus.UCSC.galGal3) |
|
| 65 |
+ library(BSgenome.Hsapiens.UCSC.hg19) |
|
| 65 | 66 |
## dotplot for Axt object |
| 66 | 67 |
fn <- file.path(system.file("extdata", package="CNEr"),
|
| 67 | 68 |
"chr4.hg19.galGal3.net.axt.gz") |
| 68 | 69 |
axt <- readAxt(fn) |
| 69 |
- firstSeqlengths <- seqlengths(fetchChromSizes("hg19"))
|
|
| 70 |
- secondSeqlengths <- seqlengths(fetchChromSizes("galGal3"))
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|
| 70 |
+ firstSeqlengths <- seqlengths(BSgenome.Hsapiens.UCSC.hg19) |
|
| 71 |
+ secondSeqlengths <- seqlengths(BSgenome.Ggallus.UCSC.galGal3) |
|
| 71 | 72 |
firstChrs <- c("chr4")
|
| 72 | 73 |
secondChrs <- c("chr4")
|
| 73 | 74 |
syntenicDotplot(axt, firstSeqlengths, secondSeqlengths, |
| ... | ... |
@@ -11,8 +11,10 @@ test_that("test_ceScan", {
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| 11 | 11 |
bedDanRer10Fn <- file.path(system.file("extdata", package="CNEr"),
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| 12 | 12 |
"filter_regions.danRer10.bed") |
| 13 | 13 |
bedDanRer10 <- readBed(bedDanRer10Fn) |
| 14 |
- qSizesHg38 <- fetchChromSizes("hg38")
|
|
| 15 |
- qSizesDanRer10 <- fetchChromSizes("danRer10")
|
|
| 14 |
+ library(BSgenome.Drerio.UCSC.danRer10) |
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| 15 |
+ library(BSgenome.Hsapiens.UCSC.hg38) |
|
| 16 |
+ qSizesHg38 <- seqinfo(BSgenome.Hsapiens.UCSC.hg38) |
|
| 17 |
+ qSizesDanRer10 <- seqinfo(BSgenome.Drerio.UCSC.danRer10) |
|
| 16 | 18 |
|
| 17 | 19 |
windows <- c(50L, 50L, 50L) |
| 18 | 20 |
identities <- c(45L, 48L, 49L) |