multipe InCurrentLociRun columns in Summary_of_Data.csv

[seb-mueller]

Whilst cleaning up code, I found that reading in Summary_of_Data.csv gave me a warning (below).

Indeed, there are 2 identical columns and the one we are selecting for seems to be based on the first one:

> meta <- read_csv(file.path(gitdir, "Summary_of_Data.csv"))
Parsed with column specification:
cols(
  .default = col_character(),
  Replicate = col_integer()
)
See spec(...) for full column specifications.
Warning message:
Duplicated column names deduplicated: 'InCurrentLociRun' => 'InCurrentLociRun_1' [19]
> table(meta$In
meta$InternalExternal           meta$InCurrentLociRun           meta$InCurrentLociRun_safe      meta$InCurrentLociRun_1         meta$InCurrentLociRun_smallset
> table(meta$In
meta$InternalExternal           meta$InCurrentLociRun           meta$InCurrentLociRun_safe      meta$InCurrentLociRun_1         meta$InCurrentLociRun_smallset
> table(meta$InCurrentLociRun)

 No Yes
 24 139
> table(meta$InCurrentLociRun_1)

 No Yes
 18 145
> aD$
aD$
> aD
An object of class "alignmentData"
21512534 rows and 139 columns

Slot "libnames":
  [1] "SL16"      "SL17"      "SL60"      "SL74"      "SL75"      "SL76"      "SL139"     "SL140"
  [9] "SL141"     "SL142"     "SL143"     "SL144"     "SL145"     "SL146"     "SL165_1"   "SL165_2"
 [17] "SL166"     "SL184"     "SL185"     "SL186"     "SL187"     "SL254"     "SL255"     "SL256"
 [25] "SL257"     "SL165"     "SL304"     "SL305"     "SL306"     "SL307"     "SL308"     "SL379"
 [33] "SL380"     "SL390"     "SL391"     "SL392"     "SL393"     "SL2108"    "SL2121"    "SL2122"
 [41] "SL2123"    "SL2124"    "SL2125"    "SL14"      "SL2178"    "SL2180"    "SL2179"    "SL2181"
 [49] "SL2182"    "SL2183"    "SL2184"    "SL2185"    "SL2186"    "SL2187"    "SL2188"    "SL2189"
 [57] "SL2190"    "SL2191"    "SL2192"    "SL2193"    "SL2194"    "SL2195"    "SL2196"    "SL2197"
 [65] "SL2198"    "SL2199"    "SL2200"    "SL2201"    "SL2202"    "SL2203"    "SL2204"    "SL2205"
 [73] "SL2206"    "SL2207"    "SL2208"    "SL2209"    "SL2210"    "SL2211"    "SL2212"    "SL2213"
 [81] "SL2214"    "SL2215"    "SL2216"    "SL2217"    "SL2218"    "SL2219"    "SL2220"    "SL2221"
 [89] "SL2222"    "SL2223"    "SL2224"    "SL2225"    "SL2298"    "SL2299"    "SL2300"    "SL2301"
 [97] "SL2302"    "SL2303"    "SL2304"    "SL2305"    "SL2306"    "SL2307"    "SL2308"    "SL2309"
[105] "SL2310"    "SL2311"    "SL2312"    "SL2313"    "SL2314"    "SL2315"    "SL2316"    "SL2317"
[113] "SL2318"    "SL2319"    "SL2320"    "SL2321"    "SL2322"    "SL2323"    "SL2324"    "SL2325"
[121] "SL2326"    "SL2327"    "SL2328"    "SL2329"    "SL2330"    "SL2331"    "SL2332"    "SL2333"
[129] "SL2404"    "SL2405"    "SL2406"    "SL2407"    "SL2408"    "SL2409"    "GSM803103" "GSM803104"
[137] "GSM803105" "GSM183546" "GSM176482"

I hope we are not selecting on the wrong one, could you double check in the Indeed, https://github.com/seb-mueller/chlamy_locus_map/blob/master/Summary_of_Data.csv this selection is the one we had in mind?

[nmatthews323]

I think we've selected the wrong one, I don't know how this has happened... I'm so sorry if we have. You about for me to give you a ring?

[nmatthews323]

I've had a look back through email trails, the last email we discussed this in was on the 25th July, this column was initially called "safe2", but in this commit I seem to have changed it to "InCurrentLociRun" but neglecting to remove the original one...

[nmatthews323]

Looks good :)