Hi everyone,

I am using a snpStats to analyze my RAD sequencing data. I created a snpMatrix in Variant Annotation using the MatrixToSnpMatrix function. Then I explored the SnmMatrix in snpStats but got a following error:

> snpsum <- col.summary(res)
Error in col.summary(res) : not a SnpMatrix object

I tried row.summary function and got the same error. Please, advice me what this error mean and how to fix it. Below is my code in snpStats.

Will be very grateful for any suggestions.

Regards,

Tereza

........................................................................................
> library (snpStats)
Error in library(hexbin) : there is no package called ‘hexbin’
> show (res)
$genotypes
A SnpMatrix with  10 rows and  50581 columns
Row names:  Rodriguez_Lizard_1240_sequence_1_pileup.txt ... Rodriguez_Lizard_623_sequence_1_pileup.txt 
Col names:  RADid_0000001_depth_39:0000000058 ... RADid_0078132_depth_33:0000000081 

$map
DataFrame with 505810 rows and 4 columns
                                snp.names       allele.1           allele.2
                              <character> <DNAStringSet> <DNAStringSetList>
1       RADid_0000001_depth_39:0000000058              C           ########
2      RADid_0000003_depth_152:0000000007              G           ########
3      RADid_0000003_depth_152:0000000034              G           ########
4      RADid_0000003_depth_152:0000000046              T           ########
5       RADid_0000010_depth_57:0000000010              T           ########
6       RADid_0000010_depth_57:0000000019              G           ########
7       RADid_0000010_depth_57:0000000020              T           ########
8       RADid_0000010_depth_57:0000000059              G           ########
9       RADid_0000010_depth_57:0000000062              C           ########
...                                   ...            ...                ...
505802 RADid_0078128_depth_175:0000000033              C           ########
505803 RADid_0078128_depth_175:0000000041              G           ########
505804  RADid_0078129_depth_31:0000000017              T           ########
505805  RADid_0078129_depth_31:0000000048              C           ########
505806  RADid_0078129_depth_31:0000000062              C           ########
505807  RADid_0078132_depth_33:0000000025              T           ########
505808  RADid_0078132_depth_33:0000000033              C           ########
505809  RADid_0078132_depth_33:0000000044              C           ########
505810  RADid_0078132_depth_33:0000000081              C           ########
          ignore
       <logical>
1           TRUE
2           TRUE
3           TRUE
4           TRUE
5           TRUE
6          FALSE
7          FALSE
8          FALSE
9           TRUE
...          ...
505802      TRUE
505803     FALSE
505804      TRUE
505805      TRUE
505806      TRUE
505807      TRUE
505808      TRUE
505809      TRUE
505810      TRUE

> summary (res)
          Length Class     Mode
genotypes 505810 SnpMatrix raw 
map            4 DataFrame S4  
> snpsum <- col.summary(res)
Error in col.summary(res) : not a SnpMatrix object
> 
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