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WubingZhang / MAGeCKFlute

Integrative analysis pipeline for pooled CRISPR functional genetic screens
https://github.com/WubingZhang/MAGeCKFlute
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Error in open.connection(file, "rt"): cannot open the connection #7

Open xie186 opened 3 years ago

xie186 commented 3 years ago

R package version:

attached packages:
[1] MAGeCKFlute_1.10.0  BiocManager_1.30.10

Code:

file3 = file.path(system.file("extdata", package = "MAGeCKFlute"),
                  "testdata/mle.gene_summary.txt")
# Read and visualize the file format
gdata = read.delim(file3, check.names = FALSE)
head(gdata)
gdata = ReadBeta(file3)
head(gdata)
FluteMLE(file3, treatname="plx", ctrlname="dmso", proj="Test_V1.10.0", organism="hsa")

Error message:

2020-11-24 00:35:13 # Create output dir and pdf file...

2020-11-24 00:35:21 # Transform id to official human gene name ...

35 genes fail to convert into Entrez IDs: 8-Sep, 2-Mar, RP4-805N21.1, AC003682.1, CTC-360G5.1, AC118274.1, 3-Sep, RP4-788L13.1, 5-Sep, 1-Mar, RP11-543D5.3, RP11-24B21.1, RP11-528L24.3, AC024575.1, AC069257.9, 6-Sep, RP11-122A3.2, RP11-152O14.5, AC026458.1, RP11-87C12.2, 4-Mar, RP11-6F2.7, 4-Sep, RP4-697K14.7, 6-Mar, AC011443.1, AC008073.5, 3-Mar, CTD-3148I10.1, PRAMEF16, RP4-811H24.6, 9-Mar, RP11-744I24.1, RP3-402G11.5, RP11-268F1.2

6 genes have duplicate Entrez IDs: RRM2, PLXNA1, LCOR, BHLHE40, CXorf22, NEBL

2020-11-24 00:36:04 # Enrichment analysis of GroupA and GroupB genes ...

2020-11-24 00:36:04 # Running KEGG+REACTOME+GOBP+Complex enrichment analysis

 Downloading genesets from CORUM ...

Error in open.connection(file, "rt"): cannot open the connection
Traceback:

1. FluteMLE(file3, treatname = "plx", ctrlname = "dmso", proj = "Test_V1.10.0", 
 .     organism = "hsa")
2. EnrichAB(p1$data, pvalue = pvalueCutoff, enrich_method = enrich_method, 
 .     organism = organism, limit = limit, filename = norm_method, 
 .     out.dir = outputDir3)
3. EnrichAnalyzer(geneList = geneList, universe = gg$EntrezID, method = enrich_method, 
 .     type = "KEGG+REACTOME+GOBP+Complex", organism = organism, 
 .     pvalueCutoff = pvalue, limit = limit, keytype = "entrez")
4. enrich.ORT(geneList, keytype = keytype, type = type, organism = organism, 
 .     pvalueCutoff = pvalueCutoff, limit = limit, universe = universe, 
 .     gmtpath = gmtpath, verbose = verbose)
5. gsGetter(gmtpath, type, limit, organism)
6. retrieve_gs(type = "CORUM", organism = organism)
7. read.table(unz(locfname, "allComplexes.txt"), sep = "\t", header = TRUE, 
 .     quote = "", stringsAsFactors = FALSE)
8. open(file, "rt")
9. open.connection(file, "rt")

Can you help me check what the problem is? Thanks in advance.