(inactive) bioAnno

Bioconductor

BiocManager::install("VennDetail")
   fromAnnHub(species = "celegans", install = FALSE)
.extratGO <- function(taxid = NULL, species = NULL){
    # temp file
    if(is.null(taxid)){
    taxid <- .get.species.info(species)['tax.id']
    }
    tmp<-paste(
    tempfile(),
    "gz",
    sep = "."
    )
    # import Gene to Gene Ontology from NCBI Gene database
    download.file(
    "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz",
    quiet = TRUE,
    destfile = tmp
    )
    # uncompress
    gunzip(tmp)
    # read the file (linux and windows)
    gene2go = fread(
    sub("\\.gz", "", tmp),
    verbose = FALSE,
    showProgress = FALSE
    )
    # select columns and rename
    gene2go <- unique(
    gene2go[,c(seq_len(4)), with = FALSE]
    )
    colnames(gene2go) <- c("taxid", "GID", "GO", "EVIDENCE")
    # convert columns in character
    gene2go[,
        `:=`(
        taxid = as.character(gene2go$taxid),
        GID = as.character(gene2go$GID)
        )
        ]
    # filter with taxid
    gene2go <- as.data.frame(gene2go)
    gene2go <- gene2go[gene2go$taxid == taxid,2:4]
    return(gene2go)
}
tmp<-paste(
tempfile(),
"gz",
sep = "."
)
tmp <- paste(tempfile(), "gz", sep = ".")
tempfile(fileext=".gz")
A matrix with two columns:

GID TAIR GENE ID

ENTREZID NCBI ENTREZID ID
fromAnnHub(species="ath", install=FALSE)
...
...
################################################################
Please find your annotation package in ...
/tmp/RtmpI1ySAa/org.ath.eg.db 
You can install it by using
install.packages("/tmp/RtmpI1ySAa/org.ath.eg.db,repos = NULL,type='source') 
################################################################
Here are the tables in the package org.ath.eg.db ...
gene_info genes go go_all go_bp go_bp_all go_cc go_cc_all go_mf go_mf_all map_counts map_metadata metadata path 
refseq symbol 
################################################################
library(org.ath.eg.db)
ls(2)
# [1] "org.ath.eg"          "org.ath.eg_dbconn"   "org.ath.eg_dbfile"  
# [4] "org.ath.eg_dbInfo"   "org.ath.eg_dbschema" "org.ath.eg.db"      
# [7] "org.ath.egORGANISM" 

org.ath.eg_dbschema()

Warning messages:
1: In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
2: In max(ii) : no non-missing arguments to max; returning -Inf
library(org.ath.eg.db)
ls(2)
# [1] "org.ath.eg"          "org.ath.eg_dbconn"   "org.ath.eg_dbfile"  
# [4] "org.ath.eg_dbInfo"   "org.ath.eg_dbschema" "org.ath.eg.db"      
# [7] "org.ath.egORGANISM" 

org.ath.eg_dbschema()

Warning messages:
1: In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
2: In max(ii) : no non-missing arguments to max; returning -Inf
fromAnnHub(species="ath", install=FALSE)
...
...
################################################################
Please find your annotation package in ...
/tmp/RtmpI1ySAa/org.ath.eg.db 
You can install it by using
install.packages("/tmp/RtmpI1ySAa/org.ath.eg.db,repos = NULL,type='source') 
fromEnsembl(species = "Caenorhabditis elegans", anntype="KEGG")
> fromEnsembl(species = "Caenorhabditis elegans", anntype="KEGG", install=FALSE) 
Gene Ontology are not list in your annotation database
Protein Family are not list in your annotation database
InterPro are not list in your annotation database
Reactome Pathway are not list in your annotation database
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating symbol table:
symbol table filled
Populating entrezid table:
entrezid table filled
Populating go table:
go table filled
Populating path table:
path table filled
Populating pfam table:
pfam table filled
Populating interpro table:
interpro table filled
Populating reactome table:
reactome table filled
table metadata filled

'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
Populating go_bp table:
go_bp table filled
Populating go_cc table:
Populating go_mf table:
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
Populating go_mf_all table:
Populating go_all table:
go_all table filled
Creating package in /tmp/RtmpeBkSk2/org.Caenorhabditis.eg.db 
Now deleting temporary database file
################################################################
Please find your annotation package in ...
/tmp/RtmpeBkSk2/org.Caenorhabditis.eg.db 
You can install it by using
install.packages("/tmp/RtmpeBkSk2/org.Caenorhabditis.eg.db",repos = NULL,type='source') 
################################################################
Here are the tables in the package org.Caenorhabditis.eg.db ...
entrezid gene_info genes go go_all go_bp go_bp_all go_cc go_cc_all go_mf go_mf_all interpro map_counts map_metadata metadata path pfam reactome symbol 
################################################################
Warning message:
`select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
> library(org.Caenorhabditis.eg.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Warning message:
call dbDisconnect() when finished working with a connection 
> org.Caenorhabditis.eg_dbschema()

Warning messages:
1: In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
2: In max(ii) : no non-missing arguments to max; returning -Inf

Bioconductor / Contributions

(inactive) bioAnno #1404

1. I'll start with the documentation. It has many English mistakes and also mistakes like this one in the vignette:

2. Or this one in the man page for fromAnnHub():

3. Please re-read and check carefully all your documentation (man pages and vignette) and make sure it is clear, accurate, and concise. It needs a lot of improvement.