lproks(genomes)
lproks()所属R语言包：genomes
Microbial genome projects at NCBI
在NCBI的微生物基因组计划
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Microbial genomes from Entrez genome project at NCBI.
在NCBI Entrez的基因组计划的微生物基因组。
用法----------Usage----------
data(lproks)
格式----------Format----------
A genomes data frame with observations on the following 31 variables.
一个基因组与以下31个变量的观测数据框。
pid genome project id
pid基因组项目的ID
name taxonomy name
name分类名称
status sequencing status, Complete, Assemby, or
status测序状态，完整，Assemby，或
released released date, complete and WGS genomes
released发布日期，完整和WGS基因
refseq_pid RefSeq project id
refseq_pid的RefSeq项目编号
taxid taxonomy id
taxid分类编号
kingdom kingdom
kingdom王国
group phylum or class
group门或类
size genome size (Mbp)
size基因组大小（MBP）
GC percent GC content
GC％GC含量
chromosomes number of chromosomes, complete genomes only
chromosomes染色体的数目，完整的基因组
plasmids number of plasmids, complete genomes only
plasmids质粒的数量，完整的基因组
modified modified date, complete genomes only
modified修改日期，完整的基因组只
genbank comma-separated list of GenBank accession numbers
genbank逗号分隔的列表，GenBank登录号
refseq comma-separated list of RefSeq accession numbers
refseq逗号分隔的列表的RefSeq加入号码
publication comma-separated list of PubMed ids, complete genomes only
仅publication逗号分隔的列表医学IDS，完整的基因组
center pipe-separated list of sequencing centers
center管道分隔的列表测序中心
contigs number of genome contigs. For complete
contigs基因组重叠群的数量。如需完整的
cds number of coding sequences, WGS only
cds数编码序列，唯一的WGS
url sequencing center url, WGS and In Progress
url测序中心的网址，工作组和在进展
gram gram stain
gram革兰氏染色法
shape shape
shape形状
arrange arrangement
arrange安排
endospore endospores
endospore孢子
motility motility
motility活力
salinity salinity
salinity盐度
oxygen oxygen requirement
oxygen氧气要求
habitat habitat
habitat栖息地
temp temperature preference
temp温度偏好
range temperature range
range温度范围
pathogen pathogenic in host
pathogen在宿主致病
disease disease
disease疾病
Details
详情----------Details----------
This table is constructed using all three tabs at http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi. Complete genomes and In Progress tabs are combined and then joined to the Organism Info tab. A few manual updates were also added: 725 missing released dates from GenBank assemblies were added, 178 complete genomes with assembly released dates were corrected (see complete), and genome size outliers were removed.
此表构造使用在http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi所有三个标签。完整的基因组和进展标签相结合，然后加入生物信息选项卡。几个手动更新也增加了：725失踪公布日期从GenBank组件增加了178完整的基因组大会发布日期更正（见complete），基因组大小离群被拆除。
The update(genomes) function downloads a recent copy of the table from NCBI. The number of new project IDs are reported as well as the number of project IDs removed (which are typically Assembly
update(genomes)函数表从NCBI下载最新副本。一些新的项目ID报告以及删除的项目ID（这是典型的大会
源----------Source----------
downloaded from http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
下载http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi
举例----------Examples----------
data(lproks)
lproks
#single row (long format)[单排（长格式）]
t(lproks[1,])
class(lproks)
## download stats[＃下载统计]
attributes(lproks)[c("stats", "date","url")]
summary(lproks)
## check for missing release dates[＃检查是否有遗漏的发行日期]
table2(!is.na(lproks$released), lproks$status, dnn=list("Released Date?", "Status"))
plot(lproks)
plotby(lproks, log='y', las=1)
## download recent table from NCBI[＃从NCBI下载最近表]
## Not run: update(lproks) [＃不运行：更新（lproks）]
## Yersinia genomes[＃耶尔森氏菌基因组]
yp <- subset(lproks, name %like% 'Yersinia*')
yp
summary(yp)
plotby(yp, labels=TRUE, cex=.7, lbty='n')
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 19:24:18
