yulab-smu/meshes

:stethoscope: MeSH Enrichment and Semantic analyses

meshes: MeSH Enrichment and Semantic analyses

MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.

For details, please visit https://yulab-smu.top/biomedical-knowledge-mining-book/.

✍️ Authors

Guangchuang YU https://yulab-smu.top

School of Basic Medical Sciences, Southern Medical University

meshes's Issues

background gene set for enrichMesh isn't working

I was wondering what "universe" for enrichMesh function accepts as an input as it isn't specified in the documentation found on bioconductor.

library(meshes)
x <- enrichMeSH(my.geneID3[,3], MeSHDb = "MeSH.Hsa.eg.db", database='gene2pubmed', category = 'C',universe = univ.geneID3[,2])

here, univ.geneID3[,2] is a list of entrez gene ids but I get the error

Error in validObject(.Object) :
invalid class "enrichResult" object: invalid object for slot "universe" in class "enrichResult": got class "integer", should be or extend class "character"

thanks so much!

michelle

Error in enrichMeSH: trying to get slot "result" from an object of a basic class ("NULL") with no slots

Hello,

I am trying to run the code from the basic example from the documentation of the enrichMeSH function, but this results in an error:

library(meshes)
library(AnnotationHub)
ah <- AnnotationHub()
qr_hsa <- query(ah, c("MeSHDb", "Homo sapiens"))
filepath_hsa <- qr_hsa[[1]]
db <- MeSHDbi::MeSHDb(filepath_hsa)
data(geneList, package="DOSE")
de <- names(geneList)[1:100]
x <- enrichMeSH(de, MeSHDb = db, database='gendoo', category = 'C')
--> No gene can be mapped....
--> Expected input gene ID: 
--> return NULL...
Error in enrichMeSH(de, MeSHDb = db, database = "gendoo", category = "C") : 
  trying to get slot "result" from an object of a basic class ("NULL") with no slots

I am using version 1.20.0 of the meshes package in R version 4.1.2.

gseMeSH and gseaplot issues (latest Bioconductor release)

Dear Guangchuang Yu,
Thank you for writing nice and helpful packages.
Unfortunately, when I tried to use Bioconductor release version the following bugs appeared.
Best Regards,
Daniil Sarkisyan, Researcher at Uppsala University, Sweden

require(DOSE)
require(meshes)

## this call to enrichMeSH talks in red too much, but works
data(geneList)
gene <- names(geneList)[abs(geneList) > 1.5]
x <- enrichMeSH(gene, MeSHDb = "MeSH.Hsa.eg.db", database='gendoo', category = 'C')
# Loading required package: MeSH.Hsa.eg.db
# Loading required package: MeSHDbi
# 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, xtabs
# 
# The following objects are masked from ‘package:base’:
#   
#   anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated,
# eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
# lengths, 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, which.max, which.min
# 
# 
# Attaching package: ‘MeSHDbi’
# 
# The following object is masked from ‘package:utils’:
#   
#   packageName

## this call to enrichMeSH breaks down complaining
y <- gseMeSH(gene, MeSHDb = "MeSH.Hsa.eg.db", database = 'gene2pubmed', category = "G")
# Error in GSEA_internal(geneList = geneList, exponent = exponent, nPerm = nPerm,  : 
#                          geneList should be a decreasing sorted vector...
                       
## when the complaint is resolved, it still breaks down with another error
geneS <- sort(gene, decreasing = TRUE)
y <- gseMeSH(geneS, MeSHDb = "MeSH.Hsa.eg.db", database = 'gene2pubmed', category = "G")
# preparing geneSet collections...
# GSEA analysis...
# Error in abs(stats) : non-numeric argument to mathematical function

## this function also does not work
## x[1,1] is the set "D000782"
gseaplot(gseaResult= x, geneSetID= x[1,1])
# Error: Aesthetics must be either length 1 or the same as the data (5): ymin, ymax, x

sessionInfo()
# R version 3.3.2 (2016-10-31)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 16.04.1 LTS
# 
# locale:
# [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
# [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
# [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
# [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
# 
# attached base packages:
# [1] parallel  stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] MeSH.Hsa.eg.db_1.7.0 MeSHDbi_1.10.0       BiocGenerics_0.20.0  meshes_1.0.0        
# [5] DOSE_3.0.10         
# 
# loaded via a namespace (and not attached):
# [1] Rcpp_0.12.9          plyr_1.8.4           tools_3.3.2          digest_0.6.12       
# [5] RSQLite_1.1-2        memoise_1.0.0        tibble_1.2           gtable_0.2.0        
# [9] fastmatch_1.1-0      igraph_1.0.1         DBI_0.5-1            fgsea_1.0.2         
# [13] gridExtra_2.2.1      stringr_1.1.0        S4Vectors_0.12.1     IRanges_2.8.1       
# [17] stats4_3.3.2         grid_3.3.2           qvalue_2.6.0         data.table_1.10.4   
# [21] Biobase_2.34.0       AnnotationDbi_1.36.2 BiocParallel_1.8.1   GOSemSim_2.0.4      
# [25] GO.db_3.4.0          ggplot2_2.2.1        DO.db_2.9            reshape2_1.4.2      
# [29] magrittr_1.5         MeSH.db_1.7.0        scales_0.4.1         splines_3.3.2       
# [33] assertthat_0.1       colorspace_1.3-2     stringi_1.1.2        lazyeval_0.2.0      
# [37] munsell_0.4.3