Error in SMITE package tutorial

[biovitus]

Dear Sir/Madam,

I am getting error when executing makePvalueObject function from tutorial in SMITE package. I am enclosing the output of test_annotation and error I am getting. I like to know if you can help in fixing it.

Appreciate your help.

Sincerely,

biovitus

test_annotation * Class P-Value Annotation, method Show * First 10 Expression data are shown: expression_effect expression_pvalue A1BG 0.31905997 0.835528104 A1BG-AS1 -0.77446928 0.127105406 A2M -0.36049162 0.133665150 A2M-AS1 0.34825637 0.004019176 A2ML1 0.42322933 0.441982383 A2MP1 -4.09733596 0.024239448 A4GALT 0.05462111 0.376350339 A4GNT -0.08907314 0.190395073 AA06 0.15552269 0.006156866 AAAS -0.01205622 0.087326870 First 10 rows of methylation data are shown: GRanges object with 10 ranges and 5 metadata columns: seqnames ranges strand | name feature effect

| A1CF chr10 [52588252, 52588253] \* | A1CF original 2.049 A1CF chr10 [52584012, 52584013] \* | A1CF original -12.668 A1CF chr10 [52612663, 52612664] \* | A1CF original 4.402 A1CF chr10 [52582130, 52582131] \* | A1CF original 31.446 A1CF chr10 [52641045, 52641046] \* | A1CF original 23.319 A1CF chr10 [52631272, 52631273] \* | A1CF original 0.220 A1CF chr10 [52601040, 52601041] \* | A1CF original 80.586 A1CF chr10 [52588252, 52588253] \* | A1CF body 2.049 A1CF chr10 [52584012, 52584013] \* | A1CF body -12.668 A1CF chr10 [52612663, 52612664] \* | A1CF body 4.402 pval type A1CF 0.17204032 methylation A1CF 0.18500037 methylation A1CF 0.08505655 methylation A1CF 0.18568468 methylation A1CF 0.03923139 methylation A1CF 0.54036951 methylation A1CF 0.26642095 methylation A1CF 0.17204032 methylation A1CF 0.18500037 methylation A1CF 0.08505655 methylation --- seqinfo: 2 sequences from an unspecified genome; no seqlengths ******\* End Show (pvalue.object) ******\* test_annotation <- makePvalueObject(test_annotation, - effect_directions = c(methylation_promoter = "decrease", - methylation_body = "decrease", - methylation_h3k4me1 = "bidirectional")) Error in validObject(.Object) : invalid class “PvalueObject” object: invalid object for slot "genes" in class "PvalueObject": got class "factor", should be or extend class "character"

[radiohboy]

Hi, Thanks for contacting us. The error indicates that dataset (even our test data) is being input as a factor instead of a character/numeric. Can you verify that you used the options(stringsAsFactors=F) command before loading the data and using the package? We are working on a better way to handle these factor-character issues for the release.

[biovitus]

Dear Sir,

Thank you for your reply. I did not use the options(stringsAsFactors=F) before using the package and loading the data. After using it I did not get the error mentioned in my initial comment.

Appreciate your help.

Sincerely,

biovitus

[radiohboy]

Great. Yeah its an annoying issue but thats the only work-around that is reliable. The program is part of the next Bioconductor release. If you will be testing it on your data, we would love to know how your results look. Please contact us with any general feedback through Github.