countReadsAnnotated(girafe)
countReadsAnnotated()所属R语言包：girafe
Sum up aligned reads per category of genome feature
总结对齐读取每类基因组功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A function to sum up aligned reads per category of genome feature (i.e. gene, ncRNA, etc.).
每类基因组功能（即基因，非编码RNA等）读取函数总结对齐。
用法----------Usage----------
countReadsAnnotated(GI, M, typeColumn="type", fractionGI=0.7,
mem.friendly=FALSE, showAllTypes=FALSE)
参数----------Arguments----------
参数：GI
object of class AlignedGenomeIntervals
对象类AlignedGenomeIntervals
参数：M
Annotation object of class Genome_intervals_stranded or Genome_intervals; describes the genomic coordinates of annotated genome features, such as genes, miRNAs, etc.
注释对象的类Genome_intervals_stranded或Genome_intervals;介绍了注释的基因组功能基因组坐标，如基因的miRNA，等
参数：typeColumn
string; which column of the annotation object M describes the type of the genome feature
字符串列的注释对象M描述类型的基因组功能
参数：fractionGI
which fraction of the intervals in object GI are required to ovelap with a feature in M in order to be considered to correspond to that feature.
在对象的间隔部分GI需要在功能ovelap M为了被视为符合该功能。
参数：mem.friendly
logical; should a version which requires less memory but takes a bit longer be used
逻辑;应版本，它需要较少的内存，但需要多一点的时间用于
参数：showAllTypes
logical; should a table of genome feature types in M be displayed?
逻辑;基因组功能类型在表M显示？
Details
详情----------Details----------
The read counts are summed up over each type of genome feature, and the read counts are normalised by their number of genomic matches. For example if a read has two matches in the genome, but only one inside a miRNA, it would count 0.5 for miRNAs.
读取计数总结了每种类型的基因组功能，其基因组比赛标准化和读取计数。例如，如果一个只读在基因组的两场比赛，但只在一个miRNA之一，它会计算miRNA的0.5。
值----------Value----------
A named numeric vector which gives the summed read counts for each supplied type of genome feature.
一个名为“数字向量给每个基因的功能提供的类型总结阅读计数。
作者（S）----------Author(s)----------
J Toedling
举例----------Examples----------
A <- AlignedGenomeIntervals(
start=c(1,8,14,20), end=c(5,15,19,25),
chromosome=rep("chr1", each=4),
strand=c("+","+","+","+"),
sequence=c("ACATT","TATCGGAC","TCGGACT","GTAACG"),
reads=c(7L, 2L, 4L, 5L) )
M2 <- new("Genome_intervals_stranded",
rbind(c(2,6), c(1,15), c(20,30)),
closed = matrix(TRUE, ncol=2, nrow=3),
annotation = data.frame(
seq_name= factor(rep("chr1", 3)),
inter_base= logical(3),
strand=factor(rep("+", 3), levels=c("+","-")),
alias=c("miRNA1","gene1","tRNA1"),
type=c("miRNA","gene","tRNA")) )
if (interactive()){
grid.newpage()
plot(A, M2, chr="chr1", start=0, end=35,
nameColum="alias", show="plus")
}
countReadsAnnotated(A, M2, typeColumn="type")
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 19:52:10
