readGff3(genomeIntervals)
readGff3()所属R语言包：genomeIntervals
Make a Genome\_intervals\_stranded object from a GFF file
使基因组\ _intervals \ _stranded对象从GFF文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Make a Genome_intervals_stranded object from a gff file in gff3 format.
请在GFF文件gff3格式，从一个Genome_intervals_stranded对象。
用法----------Usage----------
readGff3(file, isRightOpen=TRUE)
参数----------Arguments----------
参数：file
The name of the gff file to read.
GFF文件名称改为。
参数：isRightOpen
Although a proper GFF3 file follows the convention of right-open intervals, improper GFF files following the right-closed convention are frequently found. Set isRightOpen = FALSE in this case.
虽然适当GFF3文件如下右开区间公约，不当GFF文件后，封闭的权利公约经常发现。设置isRightOpen = FALSE在这种情况下。
Details
详情----------Details----------
The file must follow gff3 format specifications as in http://www.sequenceontology.org/gff3.shtml. The file is read as a table. Meta-information (lines starting with \#\#\#) are not parsed. A “.” in, for example, the gff file's score or frame field will be converted to NA. When the GFF file follows the right-open interval convention (isRightOpen is TRUE), then GFF entries for which end base equals first base are recognized as zero-length features and loaded as inter_base intervals. Strand entries in the file are expected to be '.', '?', '+' or '-'. The two first are mapped to NA. It can be that readGff3 is able to construct a Genome_intervals_stranded object from the input file, although not valid. A warning message is then generated and the constructed object is returned to allow inspection of it.
该文件必须遵循如在http://www.sequenceontology.org/gff3.shtml gff3格式规范。该文件是只读表。元信息（行开始\＃\＃\＃）不解析。一个“。”，例如，GFF文件的得分或框架的领域将被转换为NA。当GFF文件如下右开区间公约（isRightOpenTRUE），然后GFF项为碱基等于一垒被确认为长度为零的特点和inter_base加载的间隔。预计在文件中的股项是，+或。？ - 。两人第一次被映射到NA。它可以是readGff3是能够构建从输入文件Genome_intervals_stranded对象，虽然没有有效的。然后生成一个警告消息和构造的对象被返回到允许它的检查。
值----------Value----------
A Genome_intervals_stranded object image of the gff file. The GFF3 fields seqid, source, type, score, strand, phase and attributes are stored in the annotation slot and renamed as seq_name, source, type, score, strand, phase and gffAttributes respectively.
一个Genome_intervals_strandedGFF文件对象的图像。 GFF3领域seqid，source，type，score，strand，phase和attributes存储在annotation槽，并更名为seq_name，source，type，score，strand，phase和gffAttributes分别。
注意----------Note----------
Potential FASTA entries at the end of the file are ignored.
在文件的末尾潜在的FASTA格式的条目将被忽略。
参见----------See Also----------
The functions getGffAttribute and parseGffAttributes for parsing GFF attributes.
职能getGffAttribute和parseGffAttributes解析GFF属性的。
举例----------Examples----------
# Get file path[获取文件路径]
libPath <- installed.packages()["genomeIntervals", "LibPath"]
filePath <- file.path(
libPath,
"genomeIntervals",
"example_files"
)
# Load SGD gff[载入新元GFF]
# SGD does not comply to the GFF3 right-open interval convention[新元不符合的GFF3右开区间公约]
gff <- readGff3( file.path( filePath, "sgd_simple.gff"), isRightOpen = FALSE)
head(gff,10)
head(annotation(gff),10)
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 19:21:24
