The readVcf function apparently works fine on phase 3 1000 Genomes data (see output at the bottom). However, when I try to use some functions mentioned in the manual, I get various error messages. 

head(rowRanges(vcf), 3)
Error in head(rowRanges(vcf), 3) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': Error in rowRanges(vcf) : Argument 'x' must be a matrix or a vector.

or even empty outputs, such as: 

geno(vcf)
List of length 0
names(0): 
> sapply(geno(vcf), class)
named list()
> info(vcf)[1:4, 1:5]
DataFrame with 4 rows and 5 columns
          CIEND         CIPOS          CS       END IMPRECISE
  <IntegerList> <IntegerList> <character> <integer> <logical>
1         NA,NA         NA,NA          NA        NA     FALSE
2         NA,NA         NA,NA          NA        NA     FALSE
3         NA,NA         NA,NA          NA        NA     FALSE
4         NA,NA         NA,NA          NA        NA     FALSE

Appendix:

 fl <-  ("ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz")
> vcf <- readVcf(fl, "hg38")
> vcf
class: CollapsedVCF 
dim: 1103547 0 
rowData(vcf):
  GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
  DataFrame with 27 columns: CIEND, CIPOS, CS, END, IMPRECISE, MC, MEINFO, MEND, MLEN, MSTART, SVLEN,...

Hi,

The 'rowData' name (slot, argument and accessor) has recently been replaced with 'rowRanges' in the SummarizedExperiment class which the VCF class inherits from. If you're using devel you should be using rowRanges(); for release use rowData().

Please make sure you're packages are up to date with biocLite() and try again. If you still get an error provide the output of sessionInfo() so we can see what versions you're using.

Valerie

hi, I cannot reproduce the problem, your code works fine with my R/BioC installation and my local copy of the 1000 Genomes Project genotype VFC files:

library(VariantAnnotation)

vcf <- readVcf("ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz", genome="hg19")
vcf

class: CollapsedVCF
dim: 1103547 0
rowRanges(vcf):
  GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
  DataFrame with 27 columns: CIEND, CIPOS, CS, END, IMPRECISE, MC, MEINFO, MEND, MLEN, MSTART, SVLEN, SVTYPE, TSD, AC, AF, N...
info(header(vcf)):
                 Number Type    Description                                                                                    
   CIEND         2      Integer Confidence interval around END for imprecise variants                                          
   CIPOS         2      Integer Confidence interval around POS for imprecise variants                                          
   CS            1      String  Source call set.                                                                               
   END           1      Integer End coordinate of this variant                                                                 
   IMPRECISE     0      Flag    Imprecise structural variation                                                                 
   MC            .      String  Merged calls.                                                                                  
   MEINFO        4      String  Mobile element info of the form NAME,START,END<POLARITY; If there is only 5' OR 3' support f...
   MEND          1      Integer Mitochondrial end coordinate of inserted sequence                                              
   MLEN          1      Integer Estimated length of mitochondrial insert                                                       
   MSTART        1      Integer Mitochondrial start coordinate of inserted sequence                                            
   SVLEN         .      Integer SV length. It is only calculated for structural variation MEIs. For other types of SVs; one ...
   SVTYPE        1      String  Type of structural variant                                                                     
   TSD           1      String  Precise Target Site Duplication for bases, if unknown, value will be NULL                      
   AC            A      Integer Total number of alternate alleles in called genotypes                                          
   AF            A      Float   Estimated allele frequency in the range (0,1)                                                  
   NS            1      Integer Number of samples with data                                                                    
   AN            1      Integer Total number of alleles in called genotypes                                                    
   EAS_AF        A      Float   Allele frequency in the EAS populations calculated from AC and AN, in the range (0,1)          
   EUR_AF        A      Float   Allele frequency in the EUR populations calculated from AC and AN, in the range (0,1)          
   AFR_AF        A      Float   Allele frequency in the AFR populations calculated from AC and AN, in the range (0,1)          
   AMR_AF        A      Float   Allele frequency in the AMR populations calculated from AC and AN, in the range (0,1)          
   SAS_AF        A      Float   Allele frequency in the SAS populations calculated from AC and AN, in the range (0,1)          
   DP            1      Integer Total read depth; only low coverage data were counted towards the DP, exome data were not used
   AA            1      String  Ancestral Allele. Format: AA|REF|ALT|IndelType. AA: Ancestral allele, REF:Reference Allele, ...
   VT            .      String  indicates what type of variant the line represents                                             
   EX_TARGET     0      Flag    indicates whether a variant is within the exon pull down target boundaries                     
   MULTI_ALLELIC 0      Flag    indicates whether a site is multi-allelic                                                      
geno(vcf):
  SimpleList of length 0:

head(rowRanges(vcf), 3)
GRanges object with 3 ranges and 5 metadata columns:
              seqnames               ranges strand | paramRangeID            REF             ALT      QUAL      FILTER
                 <Rle>            <IRanges>  <Rle> |     <factor> <DNAStringSet> <CharacterList> <numeric> <character>
  rs587697622       22 [16050075, 16050075]      * |         <NA>              A               G       100        PASS
  rs587755077       22 [16050115, 16050115]      * |         <NA>              G               A       100        PASS
  rs587654921       22 [16050213, 16050213]      * |         <NA>              C               T       100        PASS
  -------
  seqinfo: 86 sequences from hg19 genome

sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Fedora release 12 (Constantine)

locale:
 [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C              LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8    
 [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8    LC_PAPER=en_US.UTF8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C            LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] VariantAnnotation_1.14.1 Rsamtools_1.20.2         Biostrings_2.36.1        XVector_0.8.0           
 [5] GenomicRanges_1.20.3     GenomeInfoDb_1.4.0       IRanges_2.2.1            S4Vectors_0.6.0         
 [9] BiocGenerics_0.14.0      vimcom_1.2-3             setwidth_1.0-3           colorout_1.1-0          

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.30.1    zlibbioc_1.14.0         GenomicAlignments_1.4.1 BiocParallel_1.2.1      BSgenome_1.36.0        
 [6] tools_3.2.0             Biobase_2.28.0          DBI_0.3.1               lambda.r_1.1.7          futile.logger_1.4.1    
[11] rtracklayer_1.28.2      futile.options_1.0.0    bitops_1.0-6            RCurl_1.95-4.6          biomaRt_2.24.0         
[16] RSQLite_1.0.0           GenomicFeatures_1.20.1  XML_3.98-1.1           

the output of your call to traceback() seems incomplete to me. It should show all the intermediate function calls that lead to the error. See the following toy example:

g <- function(x) 2*x
f <- function(x) g(x)
f("hello world\n")
Error in 2 * x : non-numeric argument to binary operator
traceback()
2: g(x) at #1
1: f("hello world\n")

although if the software actually works for me, it is likely that the problem may be related to your local copy of the VCF file. Could you try to download it again and see whether it works then?

cheers,

robert.

Many thanks for your help!