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 > [[alternative HTML version deleted]]

res is a list with two elements you must use col.summary(res[[1]]) On Fri, Mar 22, 2013 at 1:00 AM, Tereza Jezkova - personal < caloprymnus@hotmail.com> wrote: > 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 > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]