count.reads(seqbias)
count.reads()所属R语言包:seqbias
Counting reads across intervals
在时间间隔计数读取
译者:生物统计家园网 机器人LoveR
描述----------Description----------
Counts the number of reads starting at each position across given
计算在整个给每个位置开始读取数
用法----------Usage----------
count.reads(reads_fn, I, sb=NULL, binary=FALSE, sum.counts=FALSE)
参数----------Arguments----------
参数:reads_fn
filename of aligned reads in BAM format
在BAM格式对齐的文件名读取
参数:I
a GRanges object giving valid genomic intervals
1农庄对象给予有效的基因组间隔
参数:sb
a seqbias object
1 seqbias对象
参数:binary
if TRUE, return a 0-1 vector, otherwise return a vector counting the number of reads mapped to each position
如果TRUE,返回0-1向量,否则返回一个向量映射到每个位置计数读取
参数:sum.counts
if TRUE return the total read count for each interval
如果TRUE返回每个区间的总阅读数
Details
详情----------Details----------
Given an indexed BAM file, this function counts the number of reads starting at each position of each provided interval. If a seqbias object is provided through the sb attribute, counts are corrected for sequence bias. The total read count for each interval is returned if sum.counts is TRUE.
此功能鉴于索引BAM的文件,计算每个区间的每个位置开始读取的数量。如果seqbias对象提供通过sb属性,计数序列偏差的纠正。返回sum.counts是TRUE每个区间总读计数。
If binary is TRUE a 0-1 vector is returned instead, where positions at which no reads are mapped are 0, and those with one or more are 1.
binary如果是TRUE 0-1向量,而不是返回,没有读取映射的位置是0,和那些与一个或多个1。
值----------Value----------
A list of numeric vectors is returned, one for each interval provided. Each vector gives an integer count of the number of reads beginning on that position.
返回一个数值向量,每间隔一个提供。每个向量给出了一个在该位置开始读取数量的整数计数。
注意----------Note----------
The BAM file provided should be indexed with 'samtools index'.
在BAM文件规定应索引“samtools指数”。
作者(S)----------Author(s)----------
Daniel Jones
<a href="mailto:dcjones@cs.washington.edu">dcjones@cs.washington.edu</a>
参见----------See Also----------
seqbias.predict
seqbias.predict
举例----------Examples----------
reads_fn <- system.file( "extra/example.bam", package = "seqbias" )
I <- GRanges( c('seq1'), IRanges( c(1), c(5000) ), strand = c('-') )
counts <- count.reads( reads_fn, I )
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注:
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