read.structure has problems with names that start with a number

[romunov]

Elizabeth posted a question she had with importing a structure file. Here is a reproducible example. Samples C_KH1059 and K_KH1834 are expected to have alleles of .33 for locus 1401_25, but are actually NA.

library(adegenet)

cat(print("		1_25	8_54	1358_15	1363_12	1368_57	1369_41	1372_14	1373_9	1377_42	1378_53	1379_10	1382_37	1386_27	1398_46	1400_9	1401_25	1403_13	1404_17	1409_42	1416_48	1419_11	1421_14	1423_5	1424_74	1426_55	1429_46	1432_23	1435_30	1436_7	1438_9	1443_37
A_KH1584	A	1	4	4	1	1	3	2	4	4	2	3	3	2	4	1	3	1	1	2	3	1	4	4	3	2	2	3	4	4	4	2
A_KH1584	A	1	4	4	1	1	3	2	4	4	4	3	3	4	4	1	3	1	3	2	3	3	4	4	3	4	2	3	4	4	4	2
C_KH1059	C	0	4	4	1	1	3	2	4	4	2	1	3	2	4	1	3	1	3	2	3	3	2	4	3	2	2	3	2	4	4	2
C_KH1059	C	0	4	4	1	1	3	2	4	4	4	3	3	2	4	1	3	1	3	2	3	3	4	4	3	2	2	3	4	4	4	2
M_KH1834	M	0	2	2	1	1	3	2	4	4	2	3	3	2	4	1	3	1	1	2	3	3	4	4	3	2	2	3	2	4	4	2
M_KH1834	M	0	4	4	1	3	3	2	4	4	2	3	3	2	4	1	3	1	3	2	3	3	4	4	3	2	4	3	4	4	4	2
M_KH1837	M	1	4	4	1	1	3	2	4	4	0	3	3	2	2	1	3	1	1	2	3	3	4	4	3	4	2	3	4	4	4	2
M_KH1837	M	1	4	4	1	3	3	2	4	4	0	3	3	4	4	1	3	1	3	2	3	3	4	4	3	4	2	3	4	4	4	2"), 
    file = "elizabeth_starts_with_number.stru")

xy1 <- read.structure("elizabeth_starts_with_number.stru", NA.char="0",
                     n.ind = 4, n.loc = 31, onerowperind = FALSE,
                     col.lab = 1, col.pop = 2, row.marknames = 1,
                     sep = "\t", col.others = 0)

x1 <- tab(xy1)

# 1401_25.33 are NA but should be 1 for samples C_KH1059 M_KH1834
x1[, grepl("1401_25", colnames(x1)), drop = FALSE]

#          1401_25.33
# A_KH1584          1
# C_KH1059         NA
# M_KH1834         NA
# M_KH1837          1

If I rename the column names so that they start with a letter, things pick up.

cat(print("		X1_25	X8_54	X1358_15	X1363_12	X1368_57	X1369_41	X1372_14	X1373_9	X1377_42	X1378_53	X1379_10	X1382_37	X1386_27	X1398_46	X1400_9	X1401_25	X1403_13	X1404_17	X1409_42	X1416_48	X1419_11	X1421_14	X1423_5	X1424_74	X1426_55	X1429_46	X1432_23	X1435_30	X1436_7	X1438_9	X1443_37
A_KH1584	A	1	4	4	1	1	3	2	4	4	2	3	3	2	4	1	3	1	1	2	3	1	4	4	3	2	2	3	4	4	4	2
A_KH1584	A	1	4	4	1	1	3	2	4	4	4	3	3	4	4	1	3	1	3	2	3	3	4	4	3	4	2	3	4	4	4	2
C_KH1059	C	0	4	4	1	1	3	2	4	4	2	1	3	2	4	1	3	1	3	2	3	3	2	4	3	2	2	3	2	4	4	2
C_KH1059	C	0	4	4	1	1	3	2	4	4	4	3	3	2	4	1	3	1	3	2	3	3	4	4	3	2	2	3	4	4	4	2
M_KH1834	M	0	2	2	1	1	3	2	4	4	2	3	3	2	4	1	3	1	1	2	3	3	4	4	3	2	2	3	2	4	4	2
M_KH1834	M	0	4	4	1	3	3	2	4	4	2	3	3	2	4	1	3	1	3	2	3	3	4	4	3	2	4	3	4	4	4	2
M_KH1837	M	1	4	4	1	1	3	2	4	4	0	3	3	2	2	1	3	1	1	2	3	3	4	4	3	4	2	3	4	4	4	2
M_KH1837	M	1	4	4	1	3	3	2	4	4	0	3	3	4	4	1	3	1	3	2	3	3	4	4	3	4	2	3	4	4	4	2"), 
    file = "elizabeth_starts_with_letter.stru")

xy2 <- read.structure("elizabeth_starts_with_letter.stru", NA.char="0",
                     n.ind = 4, n.loc = 31, onerowperind = FALSE,
                     col.lab = 1, col.pop = 2, row.marknames = 1,
                     sep = "\t", col.others = 0)

x2 <- tab(xy2)
x2[, grepl("1401_25", colnames(x2)), drop = FALSE]

#          X1401_25.33
# A_KH1584           1
# C_KH1059           1
# M_KH1834           1
# M_KH1837           1

unlink("elizabeth_starts_with_letter.stru")
unlink("elizabeth_starts_with_number.stru")

[thibautjombart]

OK thanks for looking into this. I am struggling to catch up with things so won't have time to look into it, though the fix is probably an easy one.. :-/

[romunov]

I'll have a look ASAP.

[thibautjombart]

You rock!

[romunov]

The problem was in df2genind in line 322 because of partial matching some other loci became eligible to become NA candidates. For instance, locus 1_25 would also match with 1401_25. I added a more explicit matching by forcing ^ in front of the string to make sure start of the string is also matched. By adding a letter to the beginning of the locus name, this matching worked as expected. I also added a test case for this.

[thibautjombart]

This is great, I especially like the added test, thanks for this!