how is define continuous phenotype in pyseer

[sekhwal]

Hi, Please let me know, how is define continuous phenotype in pyseer phyD-linkage.xlsx . I have tried with multiple column in input phenotype file and again with a single column file with --phenotype-column . However, the out come results are same.

####################### pyseer --phenotypes phenotypes.pheno --phenotype-column 15.deg pres bugwas-matrix.Rtab --distances mash.tsv --save-m mash_mds --max-dimensions 7> 15.deg.association.txt

[mgalardini]

Hi,

sorry, I'm not quite sure what your question exactly is, but if you want to force pyseer to interpret a phenotype column as a continuous phenotype you can do it by adding --continuous to your command.

M

[sekhwal]

Could you please edit this command for continuous phenotype where should I use --continuous. ########## pyseer --phenotypes phenotypes.pheno --pres bugwas-matrix.Rtab --distances mash.tsv --save-m mash_mds --max-dimensions 7> 15.deg.association.txt

[mgalardini]

Anywhere between pyseer and the > sign is fine

[sekhwal]

As I understood well about continuous phenotype; pyseer takes values whatever in a column of input phenotype file not a binary format. If so, do I need to RUN pyseer for EACH phenotype column in phenotype input file. Thanks.

[mgalardini]

Yes, correct, you would need to run pyseer for each column you want an association with. Use --continuous if you want to make sure pyseer treats each column as a continuous phenotype.

I'm gonna close the issue