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Diffstat (limited to 'issues')
| -rw-r--r-- | issues/add-mouse-data-from-klaus.gmi | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/issues/add-mouse-data-from-klaus.gmi b/issues/add-mouse-data-from-klaus.gmi new file mode 100644 index 0000000..b9a8efd --- /dev/null +++ b/issues/add-mouse-data-from-klaus.gmi @@ -0,0 +1,65 @@ +# Add mouse data-set + +## Tags + +* assigned: bonfacem +* priority: high +* status: in progress + +### Notes: Thu 30 Jun 2022 17:38:59 EAT + +Klaus' recently shared with us some mouse data. +Here's a snip of how that looks like: + +``` +mouse_ID BW day strain sex inf_dose animal.no. +241 CC001_m_1 100 perc_d00 CC001 m 10 FFU 1 +242 CC001_m_1 98.56 perc_d03 CC001 m 10 FFU 1 +243 CC001_m_1 NA perc_d13 CC001 m 10 FFU 1 +244 CC001_m_1 NA perc_d12 CC001 m 10 FFU 1 +245 CC001_m_1 NA perc_d10 CC001 m 10 FFU 1 +246 CC001_m_1 100.92 perc_d04 CC001 m 10 FFU 1 +247 CC001_m_1 98.08 perc_d01 CC001 m 10 FFU 1 +248 CC001_m_1 76.21 perc_d08 CC001 m 10 FFU 1 +249 CC001_m_1 93.22 perc_d05 CC001 m 10 FFU 1 +250 CC001_m_1 90.42 perc_d06 CC001 m 10 FFU 1 +``` + +I've been working on adding the above to the GN2 database. +The current challenge I have is that this data is Time Series---for the same strain, we have values indexed by time. +Also, we tag data by "animal.no." and "sex". +So for a male version of "CC001" with animal number 1, we have "CC001_m_1". +This is a problem---storing TS data---that Rob/Suheeta have highlighted in the past. +How do we go about doing this? +Currently, in GN2 we store averages of the aforementioned data. +This doesn't work out well for us: we don't have, AFAIU, a concept for "animal.no." +I would suggest we use lmdb to store this data, and work out a way to integrate it with the rest of GN2---so that we display this info on the main page. + +### Notes: Thu 30 Jun 2022 21:39:15 EAT + +Here's how to extract the data from the provided data-set: + +Just extract the data for d1, d2, d3 separately and use each day as a separate data set. + +``` +> unique(dat2$day) +[1] d0 d1 d2 d3 +Levels: d0 d1 d2 d3 + +> table(dat2$day) +d0 d1 d2 d3 +44 44 44 44 + +dat10 <- subset(dat2,dat2$day=="d1") +dat10 + +> dat10 + mouse_ID BW day +45 BXD 50_3 94.85000 d1 +46 BXD 64_1 96.36000 d1 +47 BXD 29_1 96.85000 d1 +48 BXD 40_3 97.69000 d1 +49 BXD 49_2 97.06000 d1 +50 BXD 6_5 89.03000 d1 +[...] +``` |