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mayoverse / kinship2

Pedigree creation, plotting, and analytics
GNU General Public License v2.0
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"Mismatched lengths, id and sex" #6

Closed GuyReeves closed 2 years ago

GuyReeves commented 2 years ago

Hi

What does the error ""Mismatched lengths, id and sex" indicate? I was hoping to set all sex =3 ,as I I only want to calculate "Kinship" for autosomes and I figure sex does not matter.

Thanks

Guy

head of my input file

ped id father mother sex 1 B15_25 NA NA 3 1 B22_2 NA NA 3 1 B106_1 B15_25 B22_2 3 1 B106_2 B15_25 B22_2 3 1 B106_3 B15_25 B22_2 3 1 B106_4 B15_25 B22_2 3 1 B106_5 B15_25 B22_2 3

sinnweja commented 2 years ago

Depending on what class your 'sex' variable is, the internal code could be trying to make a factor out of sex, where it sets the first one to 1. The other possibility for this error could be that you're not giving the column names correctly. Either way, it might be best to set the sex of those that are obviously fathers and mothers (those whose ids are in the "father" and "mother" column) to 1 and 2, respectively, and make sure your sex variable is numeric, rather than a factor.

GuyReeves commented 2 years ago

Ok I will check the column names which i think are correct and set all the specified mothers and fathers to 1 and 2, but the rest i shall leave as “3”.

On 17 Feb 2022, at 19:54, Jason Sinnwell @.***> wrote:

Depending on what class your 'sex' variable is, the internal code could be trying to make a factor out of sex, where it sets the first one to 1. The other possibility for this error could be that you're not giving the column names correctly. Either way, it might be best to set the sex of those that are obviously fathers and mothers (those whose ids are in the "father" and "mother" column) to 1 and 2, respectively, and make sure your sex variable is numeric, rather than a factor.

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GuyReeves commented 2 years ago

I corrected the sex as suggested and the error disappeared. Thanks Guy