R 中的 Bioconductor 入门
Paula Andrea Martinez, PhD.
Data Scientist
fastq
@ 唯一序列标识符 原始序列字符串 + 可选 ID 每个碱基的质量编码
fasta
> 唯一序列标识符 原始序列字符串
library(ShortRead) # 读取 fasta fasample <- readFasta(dirPath = "data/", pattern = "fasta") # 打印 fasample print(fasample)
library(ShortRead) # 读取 fasta fasample <- readFasta(dirPath = "data/", pattern = "fasta")
# 打印 fasample print(fasample)
class: ShortRead length: 500 reads; width: 50 cycles
# 访问器方法 methods(class = "ShortRead") # 写入 ShortRead 对象 writeFasta(fasample, file = "data/sample.fasta")
# 访问器方法 methods(class = "ShortRead")
# 写入 ShortRead 对象 writeFasta(fasample, file = "data/sample.fasta")
library(ShortRead) # 读取 fastq fqsample <- readFastq(dirPath = "data/", pattern = "fastq") # 打印 fqsample fqsample
library(ShortRead) # 读取 fastq fqsample <- readFastq(dirPath = "data/", pattern = "fastq")
# 打印 fqsample fqsample
class: ShortReadQ length: 500 reads; width: 50 cycles
# 访问器方法 methods(class = "ShortReadQ") # 写入 ShortRead 对象 writeFastq(fqsample, file = "data/sample.fastq.gz")
# 访问器方法 methods(class = "ShortReadQ")
# 写入 ShortRead 对象 writeFastq(fqsample, file = "data/sample.fastq.gz")
library(ShortRead) # 设定种子以每次得到相同的读段 set.seed(123) # 抽样 500 个碱基 sampler <- FastqSampler("data/SRR1971253.fastq", 500) # 保存 500 条读段 sample_small <- yield(sampler) # 类 ShortReadQ class(sample_small) # 长度 500 条读段 length(sample_small)
library(ShortRead)
# 设定种子以每次得到相同的读段 set.seed(123)
# 抽样 500 个碱基 sampler <- FastqSampler("data/SRR1971253.fastq", 500)
# 保存 500 条读段 sample_small <- yield(sampler)
# 类 ShortReadQ class(sample_small) # 长度 500 条读段 length(sample_small)
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