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smgogarten / GWASTools

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis
https://bioconductor.org/packages/GWASTools
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not able to generate scan annotation for snp matrix object #4

Closed treebreeder closed 4 years ago

treebreeder commented 4 years ago

Hi,

I would like to create a snp matrix object from a gds file! While I can produce a SnpAnnotationData frame without problems, I always get the warning message that no scan annotation was found! Hence, my Snp matrix has no row and coloumn names and I can't use it for further downstream analyses with SnpStats!

scanID<-getScanID(gds) scanAnnot<-scanID genoData<-GenotypeData(gds,snpAnnot=snpAnnot,scanAnnot=scanAnnot)

Error in validObject(.Object) : invalid class ?GenotypeData? object: invalid object for slot "scanAnnot" in class "GenotypeData": got class "character", should be or extend class "ScanAnnotationReader"

my scanAnnot vector looks like this: [1] "BFW_079301_P002_WC05" "BFW_079301_P002_WB06" "BFW_079301_P002_WD04" [4] "BFW_079301_P002_WE07" "BFW_079301_P001_WD10" "BFW_079301_P001_WB12" [7] "BFW_079301_P002_WH09" "BFW_079301_P002_WG10" "BFW_079301_P001_WB10" [10] "BFW_079301_P002_WF08" "BFW_079301_P002_WC03" "BFW_079301_P002_WB02" [13] "BFW_079301_P001_WH11" "BFW_079301_P002_WG09" "BFW_079301_P002_WG05" [16] "BFW_079301_P002_WF05" "BFW_079301_P001_WE11" "BFW_079301_P002_WH07" [19] "BFW_079301_P001_WB04" "BFW_079301_P001_WD11" "BFW_079301_P001_WA01"

I understood that the error message wants me to make a scanAnnotationDataframe instead of a normal data.frame, but I am not able to do it!

Any ideas? Highly appreciate the time you spend to help me

cheers

treebreeder commented 4 years ago

Well, I found a solution to this by myself by executing:

scanAnnot<-ScanAnnotationDataFrame(data.frame(scanID,stringsAsFactors = FALSE))

This obviously worked, but now I have the problem that when I execute genodata<-asSnpMatrix(genoData,snpNames = snpID) I get this: Warning message: In .local(object, varname, ...) : 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277, [... truncated]

genodata A SnpMatrix with 178 rows and 90979 columns Row names: BFW_079301_P002_WC05 ... BFW_079301_P001_WA09 Col names: ...

treebreeder commented 4 years ago

I found a solution to this: I forgot to put snpID into "snpID" and now it worked!