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Diffstat (limited to 'topics/data')
| -rw-r--r-- | topics/data/R-qtl2-format-notes.gmi | 39 |
1 files changed, 34 insertions, 5 deletions
diff --git a/topics/data/R-qtl2-format-notes.gmi b/topics/data/R-qtl2-format-notes.gmi index e0109b1..3397b5e 100644 --- a/topics/data/R-qtl2-format-notes.gmi +++ b/topics/data/R-qtl2-format-notes.gmi @@ -1,4 +1,4 @@ -# R/qtl2 Format Notes +# R/qtl2 and GEMMA Format Notes This document is mostly to help other non-biologists figure out their way around the format(s) of the R/qtl2 files. It mostly deals with the meaning/significance of the various fields. @@ -12,6 +12,39 @@ and We are going to consider the "non-transposed" form here, for ease of documentation: simply flip the meanings as appropriate for the transposed files. +To convert between formats we should probably use python as that is what can use as 'esperanto'. + +## Control files + +Both GN and R/qtl2 have control files. For GN it basically describes the individuals (genometypes) and looks like: + +```js +{ + "mat": "C57BL/6J", + "pat": "DBA/2J", + "f1s": ["B6D2F1", "D2B6F1"], + "genofile" : [{ + "title" : "WGS-based (Mar2022)", + "location" : "BXD.8.geno", + "sample_list" : ["BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9", "BXD11", "BXD12", "BXD13", "BXD14", "BXD15", "BXD16", "BXD18", "BXD19", "BXD20", "BXD21", "BXD22", "BXD23", "BXD24", "BXD24a", "BXD25", "BXD27", "BXD28", "BXD29", "BXD30", "BXD31", "BXD32", "BXD33", "BXD34", "BXD35", "BXD36", "BXD37", "BXD38", "BXD39", "BXD40", "BXD41", "BXD42", "BXD43", "BXD44", + ...]}]} +``` + +In gn-guile this gets parsed in gn/data/genotype.scm to fetch the individuals that match the genotype and phenotype layouts. + +## pheno files and phenotypes + +The standard GEMMA input files are not very good for trouble shooting. R/qtl2 has at least the individual or genometype ID for every line: + +``` +id,bolting_days,seed_weight,seed_area,ttl_seedspfruit,branches,height,pc_seeds_aborted,fruit_length +MAGIC.1,15.33,17.15,0.64,45.11,10.5,NA,0,14.95 +MAGIC.2,22,22.71,0.75,49.11,4.33,42.33,1.09,13.27 +MAGIC.3,23,21.03,0.68,57,4.67,50,0,13.9 +``` + +This is a good standard and can match with the control files. + ## geno files > The genotype data file is a matrix of individuals × markers. The first column is the individual IDs; the first row is the marker names. @@ -22,10 +55,6 @@ For GeneNetwork, this means that the first column contains the Sample names (pre The first column of the gmap/pmap file contains genetic marker values. There are no Individuals/samples (or strains) here. -## pheno files - -The first column is the list of individuals (samples/strains) whereas the first column is the list of phenotypes. - ## phenocovar files These seem to contain extra metadata for the phenotypes. |