【佳学基因人工智能】RNA测序数据的信息分析——基因解码信息源的准备
人的基因信息解码策略
人的基因信息解码有两种策略,一是数据库比对策略,二是基因解码策略。数据库比对策略只能用数据库中记录过的案例。由于人的特殊性,常规的基因检测无法发现临床中遇到的病人,所以查找基因病的致病原因,基因解码策略要优与数据库比对的基因检测策略。RNAseq是基因解码策略中获取原始信息并进行后续的重要一步。
分析工具的选择
佳学基因出与培训基因检测公司的目的,将使用小鼠参考基因组的一小部分(染色体1)来演示如何使用R进行高通量测序数据的比对和计数。将测序数据映射到基因组是一项非常重要的任务,并且有许多不同的比对工具可用,例如bowtie,topHat、STAR和Rsubread。根据佳学基因基因信息分析中心的实际测定,Rsubread是唯一可以在R中运行的基因信息比对分析工具。大多数对齐工具都是在linux环境中运行的,并且计算量非常大。大多数比对任务需要比普通笔记本电脑更大的计算机,因此通常在类似linux的环境中的服务器上完成原始数据的读取和比对。在这里,佳学基因的生物信息培训学员只将从智能分析老师准备的小鼠泌乳数据集中的每个样本抽取1000个数据,学习过程将比对1号染色体。因为佳学基因的主要目的是为了让基因检测机构的技术人员可以尝试使用RStudio笔记本电脑方便的进行数据分析。
软件包的安装:
不能从R中直接安装:会出现下面的结果:
install.packages(“Rsubread”)
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
将程序包安装入‘C:/Users/yunli/Documents/R/win-library/4.1’
(因为‘lib’没有被指定)
Warning in install.packages :
package ‘Rsubread’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
我们对Markdown
而应当运行如下代码:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rsubread")
出现如下信息:
https://cran.rstudio.com/bin/windows/Rtools/
将程序包安装入‘C:/Users/yunli/Documents/R/win-library/4.1’
(因为‘lib’没有被指定)
trying URL ‘https://cran.rstudio.com/bin/windows/contrib/4.1/BiocManager_1.30.16.zip’
Content type ‘application/zip’ length 328795 bytes (321 KB)
downloaded 321 KB
package ‘BiocManager’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\yunli\AppData\Local\Temp\Rtmpuaqk8c\downloaded_packages
要求更新部分功能
The downloaded binary packages are in
C:\Users\yunli\AppData\Local\Temp\Rtmpuaqk8c\downloaded_packages
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.1.2/library
packages:
class, foreign, MASS, Matrix, nlme, nnet, spatial
Old packages: ‘broom’, ‘DBI’, ‘fansi’, ‘openssl’
Update all/some/none? [a/s/n]:
更新:键盘上敲入:a
有二进制版本的,但源代码版本是后来的:
binary source needs_compilation
fansi 0.5.0 1.0.0 TRUE
Binaries will be installed
trying URL ‘https://cran.rstudio.com/bin/windows/contrib/4.1/broom_0.7.11.zip’
Content type ‘application/zip’ length 1814717 bytes (1.7 MB)
downloaded 1.7 MB
trying URL ‘https://cran.rstudio.com/bin/windows/contrib/4.1/DBI_1.1.2.zip’
Content type ‘application/zip’ length 741837 bytes (724 KB)
downloaded 724 KB
trying URL ‘https://cran.rstudio.com/bin/windows/contrib/4.1/fansi_0.5.0.zip’
Content type ‘application/zip’ length 248710 bytes (242 KB)
downloaded 242 KB
trying URL ‘https://cran.rstudio.com/bin/windows/contrib/4.1/openssl_1.4.6.zip’
Content type ‘application/zip’ length 3987697 bytes (3.8 MB)
downloaded 3.8 MB
package ‘broom’ successfully unpacked and MD5 sums checked
package ‘DBI’ successfully unpacked and MD5 sums checked
package ‘fansi’ successfully unpacked and MD5 sums checked
package ‘openssl’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\yunli\AppData\Local\Temp\Rtmpuaqk8c\downloaded_packages
软件包安装成功
检查是否可以正常调用Rsubread
library(Rsubread)