R语言 seqbias包 kmer.freq()函数中文帮助文档(中英文对照)

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kmer.freq(seqbias)
kmer.freq()所属R语言包：seqbias

                                        Measuring positional kmer frequencies
                                         测量位置kmer频率

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Given a sample of sequences and corresponding read counts, produce a table giving the position kmer frequencies relative to read starts
鉴于样本序列和相应的读取计数，产生频率相对的位置kmer读表开始


用法----------Usage----------


kmer.freq(seqs, counts, L = 50, R = 50, k = 1)



参数----------Arguments----------

参数：seqs
a list of DNAString objects.
DNAString对象名单。


参数：counts
a list of numeric vectors.
数值向量。


参数：L
how many positions to the left of the read start to consider
多少位置到左的阅读开始考虑


参数：R
how many positions to the right of the read start to consider
如何以正确的阅读开始考虑许多职位


参数：k
the size of each kmer
每个kmer的大小


Details

详情----------Details----------

Sequences and read counts are used to produce a table of aggregate kmer frequencies for each position relative to the read start. The position on which the read starts is numbered 0, positions to the left of the read are negative, and those to the right are positive.
序列和读取计数是用来产生每个位置相对的阅读开始的总kmer频率表。开始读的编号为0，位置到左读的立场是否定的，这些权利是积极的。

The sequences and counts can be generated with the provided functions scanFa and count.reads, respectively. The reverse complement of sequences on the negative strand obtained from scanFa should be used. To properly visualize bias a relatively large random sample of intervals should be generated.
所提供的功能scanFa和count.reads，分别可以生成序列和计数。从scanFa应使用取得的负链上的序列反向互补。要正确形象化偏见产生一个比较大的间隔随机抽样应。


值----------Value----------

A data frame is returned with columns pos, seq, and freq. Where pos gives the position relative to te read start, seq gives the kmer, and freq gives the frequency of that kmer.
列返回一个数据框pos，seq，freq。凡pos给出的相对位置对TE读开始，seq给的kmer，freq给人该kmer的频率。


作者（S）----------Author(s)----------



Daniel Jones
<a href="mailto:dcjones@cs.washington.edu">dcjones@cs.washington.edu</a>




参见----------See Also----------

count.reads
count.reads


举例----------Examples----------


  library(Rsamtools)
  reads_fn <- system.file( "extra/example.bam", package = "seqbias" )
  ref_fn <- system.file( "extra/example.fa", package = "seqbias" )

  I <- GRanges( c('seq1'), IRanges( c(1), c(5000) ), strand = c('-') )

  ref_f <- FaFile( ref_fn )
  open.FaFile( ref_f )

  seqs <- scanFa( ref_f, I )

  neg_idx <- as.logical( I@strand == '-' )
  seqs[neg_idx] <- reverseComplement( seqs[neg_idx] )

  counts <- count.reads( reads_fn, I )

  freqs <- kmer.freq(seqs, counts, L = 30, R = 30, k = 2)

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
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