Loading in DArT data

[Soleille Miller]

I've been trying to use gl.read.dart to read in my SNP data in 1 row format. I keep getting this error: 

Starting gl.read.dart Starting utils.read.dart Topskip not provided. Setting topskip to 6 . Reading in the SNP data Detected 1 row format. Added the following locus metrics: MarkerName AlleleSequenceRef AlleleSequenceAlt Variant CallRate OneRatioRef OneRatioSnp FreqHomRef FreqHomSnp FreqHets PICRef PICSnp AvgPIC AvgCountRef AvgCountSnp RatioAvgCountRefAvgCountSnp . Error in `$<-.data.frame`(`*tmp*`, "clone", value = character(0)) : replacement has 0 rows, data has 300

I double checked that my metadata genotype ids were in the same order as the dart SNP file. They are identical so there are no differences in the characters either. I spent a long time looking and troubleshooting and still could not get it to work. Please let me know what I should do. 

Kind regards, 

Soleille 

[Jose Luis Mijangos]

Hi Solleille,

The subset of the DArT report you sent me has a different format than the "normal" DArT report. For example, your DArT report has a field named "MarkerName" instead of "AlleleID". Also, your report doesn't have the field "SnpPosition". 

Please tell us whether this is a new or an old DArT report or if you know any other information that could tell us why your report has a different format. 

I have updated the function to read DArT reports to accept this format. For the moment the genlight slots "position" and "loc.all" are set as "NULL". These slots are not necessary for most functions to work. 

To use the updated function you need to install the developing version of dartR as shown below:

> devtools::install_github("green-striped-gecko/dartR@dev")

Cheers,

Luis 

[Soleille Miller]

Hi Luis, 

It could be because we did targeted sequencing with 300 SNPs. Does that change the outcome of the file?

Soleille

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[Soleille Miller]

Sorry, it's a new DArT report. I just got it about a month ago. 

[Soleille Miller]

Hey Luis, 

I got it to work, thank you so much! 

Cheers,

Soleille