pb导出数据HTML,基因注释信息导出为HTML：昨日迷惑的两种解决

昨日迷惑在这里 一次完全失败的尝试

后来发现，应该是数据库更新问题...?

> lookUp(igenes, "hgu95av2", "UNIGENE")

$`31485_at`

[1] "Hs.169284"

$`31486_s_at`

[1] "Hs.268515"

$`31487_at`

[1] "Hs.258563"

$`31488_s_at`

[1] "Hs.78771"

$`31489_at`

[1] "Hs.532632"

$`31490_at`

[1] "Hs.517898"

$`31491_s_at`

[1] "Hs.599762"

$`31492_at`

[1] "Hs.314359"

$`31493_s_at`

[1] NA

$`31494_at`

[1] NA

$`31495_at`

[1] "Hs.458346"

$`31496_g_at`

[1] NA

$`31497_at`

[1] NA

$`31498_f_at`

[1] NA

$`31499_s_at`

[1] "Hs.372679" "Hs.694258" "Hs.736230"

这时候再来一波 unlist 和 as.character 的操作的话，最后会有17个啊！！！

[1] "Hs.169284" "Hs.268515" "Hs.258563" "Hs.78771" "Hs.532632"

[6] "Hs.517898" "Hs.599762" "Hs.314359" NA NA

[11] "Hs.458346" NA NA NA "Hs.372679"

[16] "Hs.694258" "Hs.736230"

于是，把 UniGene ID 和 UniProt ID 一样，以 list 格式放着。

所以接下来是第一种方法，是用 annotate 这个包里的函数 htmlpage() 解决了一切。

library(annotate)

data("sample.ExpressionSet")

igenes

library(hgu95av2.db)

gb_t

ll_t

ug_t

names(ug_t)

sp_t

names(sp_t)

for(i in 1:15) {

if(i == 9 || i == 10 || i ==12 ||

i ==13 || i == 14)

ll_t[i]

}

for(i in 1:15) {

if(i == 9 || i == 10 || i ==12 ||

i ==13 || i == 14)

sp_t[[i]][1]

}

for(i in 1:15) {

if(i == 9 || i == 10 || i ==12 ||

i ==13 || i == 14)

ug_t[[i]][1]

}

name_t

name_t

for(i in 1:length(names)) {

if(i == 9 || i == 10 || i ==12 ||

i ==13 || i == 14)

name_t[i]

}

dat

FC

pval

tstat

genelist_t

filename_t

title_t

othernames_t

head_t

"Fold Change", "Sample 1", "Sample 2", "Sample 3", "Sample 4", "Sample 5", "Sample 6",

"Sample 7", "Sample 8", "Sample 9", "Sample 10")

repository_t

htmlpage(genelist_t, filename_t, title_t, othernames_t, head_t, repository = repository_t)

完美。

第二种方法 是 Jimmy 大神写的函数，导出的 HTML 比上面的好看多了，我做了些卑微小小的修改，嵌套了一下，当然最后的结果...还需要再调整。

gene2html_altered

# GeneList = igenes;

# file = 'interested_genes_2.0.html'

library(annotate)

library(hgu95av2.db)

pb2GenB

pb2ENTZ

pb2UNIG

names(pb2UNIG)

pb2UNIP

names(pb2UNIP)

pb2GenNm

for(i in 1:15) {

if(i == 9 || i == 10 || i ==12 ||

i ==13 || i == 14)

pb2ENTZ[i]

}

for(i in 1:15) {

if(i == 9 || i == 10 || i ==12 ||

i ==13 || i == 14)

pb2UNIG[i]

}

for(i in 1:15) {

if(i == 9 || i == 10 || i ==12 ||

i ==13 || i == 14)

pb2UNIP[[i]][1]

}

for(i in 1:15) {

if(i == 9 || i == 10 || i ==12 ||

i ==13 || i == 14)

pb2UNIG[[i]][1]

}

for(i in 1:length(names)) {

if(i == 9 || i == 10 || i ==12 ||

i ==13 || i == 14)

pb2GenNm[i]

}

FC

pval

tstat

createLink

sprintf('%s',base,val) ##target="_blank"

}

gene_info

UniGene = createLink(paste0("https://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=", pb2UNIG), pb2UNIG),

LocusLink = createLink(paste0("https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=", pb2ENTZ), pb2ENTZ),

GenBank = createLink(paste0("https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&term=", pb2GenB), pb2GenB),

SwissProt = createLink(paste0("http://www.uniprot.org/uniprot/", pb2UNIP), pb2UNIP),

GeneNames = pb2GenNm,

tstatistic = round(tstat, 2),

pvalue = round(pval, 3),

FoldChange = round(FC, 1),

stringsAsFactors = F)

y

DT::saveWidget(y,file)

}

gene2html_altered(igenes,'interested_genes_2.0.html')

最后，向大家隆重推荐生信技能树的一系列干货！