X.snp-class: Class "X.snp"

In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

Description

Compact representation of data concerning single nucleotide polymorphisms (SNPs) on the X chromosome

Objects from the Class

Objects can be created by calls of the form new("snp", ..., Female=...) or by subset selection from an object of class "X.snp.matrix". Holds one row or column of an object of class "X.snp.matrix"

Slots

.Data:

The genotype data coded as 0, 1, 2, or 3. For males are coded as homozygious females

Female:

A logical array giving the sex of the sample(s)

Extends

Class "snp", directly. Class "raw", by class "snp". Class "vector", by class "snp".

Methods

coerce

signature(from = "X.snp", to = "character"): map to codes "A/A", "A/B", "B/B", "A/Y", "B/Y", or ""

coerce

signature(from = "X.snp", to = "numeric"): map to codes 0, 1, 2, or NA

coerce

signature(from = "X.snp", to = "genotype"): Yet to be implemented

show

signature(object = "X.snp"): shows character representation of the object

Author(s)

David Clayton [e-mail]

References

http://www-gene.cimr.cam.ac.uk/clayton

See Also

X.snp.matrix-class, snp.matrix-class, snp-class

Examples

data(testdata)
s <- Xchromosome[,1]
class(s)
s

Example output

[1] "X.snp"
attr(,"package")
[1] "chopsticks"
A snp on the X chromosome in 214  males and  186  females
 1987   436   762  1199  1296    81  1278  1610  1121  1825   426   170   980 
"B/B" "B/Y" "B/B" "A/Y" "B/Y" "A/Y" "B/Y" "A/B" "B/Y" "B/Y" "A/Y" "B/B" "B/B" 
  911   896     4   992  1644  1634   237  1537   508   560   175  1661  1191 
"A/B" "A/Y" "A/B"    "" "B/Y" "B/Y" "B/Y" "B/Y" "A/B" "B/B" "B/Y" "A/B" "A/Y" 
 1471  1364   353  1272    43  1080   784  1250   167  1629   524  1936   287 
"A/B" "B/B" "B/Y" "A/Y" "B/Y" "A/A" "B/B" "A/B" "A/B"    "" "A/Y" "B/Y" "B/B" 
  578  1154   773  1994   208     6  1915  1230   538   615  1224  1034  1322 
"A/B" "B/Y" "B/Y" "B/Y" "B/Y" "B/Y" "A/B" "A/B" "B/Y" "A/B" "B/B" "B/B" "B/B" 
 1591    53  1814   306   247   407  1683   119  1182   755   660  1827   259 
"B/Y" "A/Y" "B/B" "A/Y" "A/B" "B/Y" "A/B" "B/B" "A/B" "B/B" "B/B" "A/B" "B/B" 
 1645   103   345   786  1740  1696   205   319  1708   931   349  1563   354 
"B/Y" "B/Y" "A/Y" "B/Y" "A/B" "B/Y" "A/B" "B/B"    "" "B/Y" "A/B" "A/Y" "A/B" 
 1110  1917  1372  1352   807   910   694  1328   154  1577   231     2   297 
"B/Y" "B/Y" "B/Y" "B/Y" "B/Y" "B/Y" "A/B" "B/Y" "B/Y" "B/B" "B/Y" "B/B" "B/Y" 
  493  1053  1454   850   464    16   339  1512  1844  1810   263   362   171 
"A/B" "B/Y" "B/Y" "B/Y" "A/B" "B/B" "B/B" "B/B" "A/A"    "" "A/A"    "" "A/B" 
  926    18  1590   386  1625   899    91  1201  1560   374  1548  1816   729 
"B/B" "A/B" "B/Y" "B/B" "B/B" "B/Y"    "" "B/B" "B/Y" "B/Y"    ""    "" "A/B" 
 1506  1762  1551  1029   970  1539   285  1961   397  1025   991   241  1775 
"A/B" "B/B"    "" "B/B" "B/B" "B/B" "B/B" "B/B" "B/B" "A/Y" "B/Y" "B/Y" "B/Y" 
  982  1300   291  1924   851   817  1131   504  1547   555  1659  1687  1052 
"B/B"    "" "B/B" "B/B" "B/Y" "B/Y" "B/Y" "B/B" "A/Y" "B/Y" "B/Y" "B/Y" "B/Y" 
 1068  1406   539  1028   257  1528   184  1148  1160  1603  1418   479   782 
"B/B" "A/B" "B/B" "B/B" "A/A" "B/Y" "B/Y" "B/Y" "B/Y" "B/Y" "B/Y" "B/Y" "B/B" 
   57  1545   787  1678   528  1384   156  1956  1922  1047  1365  1674   616 
"B/B" "A/A" "A/B" "B/B" "A/Y" "B/Y" "B/Y" "B/Y" "B/Y" "A/B" "A/B" "A/Y" "B/Y" 
  290   308   470  1482  1020  1456  1018  1614   487   803  1944   488  1218 
"B/Y" "B/Y" "A/Y" "A/B" "A/Y" "A/Y" "A/Y" "B/Y" "B/Y" "B/Y" "B/B" "B/Y" "B/Y" 
 1745  1593   141   700   429   794  1684  1942  1570    54   336  1297  1955 
"B/Y"    "" "B/Y" "B/Y" "A/Y" "A/Y" "A/Y" "B/B" "B/B" "B/B" "B/B" "A/B" "B/Y" 
 1216  1043  1933  1061   648   131  1429   197  1102   856   472  1403   726 
"A/B" "B/Y" "B/Y" "B/Y" "A/B" "A/B" "B/Y" "B/Y" "A/B" "A/Y" "A/A" "A/Y" "A/B" 
 1007  1754  1281   475  1970   128  1720   624   323   215  1639   644  1620 
"B/Y" "B/B" "B/Y"    "" "B/Y" "A/B" "B/Y" "B/B" "B/Y" "B/B" "A/B" "B/Y" "B/Y" 
  795  1022   895  1450  1141   698  1312   923  1817  1993  1903  1232   302 
"B/Y" "A/A" "B/Y" "B/Y" "A/B" "A/B" "B/B" "B/Y" "B/B" "B/B" "B/Y" "B/Y" "B/B" 
  883   846   852  1673   681  1304   512   661   900   875   340    70  1401 
"B/Y" "A/B" "A/A"    "" "B/Y" "B/B" "A/B" "B/Y" "B/Y" "B/Y" "B/Y" "A/Y" "A/A" 
 1991  1796  1700  1072  1275   858    17   160   812  1177  1192  1389   134 
"B/Y" "A/B" "A/A" "A/Y" "B/B" "B/B" "A/B" "B/Y" "A/A" "B/B" "B/Y" "B/Y" "B/Y" 
 1077    27  1989   510  1494   230  1173  1280     5  1874  1788  1183  1976 
"B/B" "B/Y" "B/Y" "B/B" "A/B" "B/Y" "B/Y" "A/Y" "A/Y" "B/B" "B/B" "A/B" "B/B" 
 1161  1882   526   669   451    42   714  1631   866  1286  1763   322    98 
"B/Y" "A/A" "B/B" "A/A" "A/B" "A/B" "B/Y" "B/B" "B/B" "A/A"    "" "B/Y" "B/B" 
 1549  1342    50  1559    75   824  1601   168   886  1478  1943  1223  1830 
"B/B" "B/Y" "A/Y" "A/B" "A/B" "A/B" "B/Y"    "" "A/A"    "" "B/Y" "B/Y" "A/B" 
 1382   485  1204  1430  1380   630   984  1404   545  1516  1442    87  1026 
"B/Y"    "" "A/Y" "A/A" "B/Y" "A/Y" "B/B" "B/B" "B/B" "B/Y" "B/Y" "B/Y" "A/Y" 
 1790   180  1499   177   380  1898   557  1837   705  1923  1058  1930   331 
"B/B" "B/Y" "B/B" "B/B" "A/B" "B/B" "A/Y" "A/Y" "A/B" "A/B" "A/Y" "B/Y" "A/Y" 
 1853   248    55   155   522  1980  1002   238  1288  1427  1180   647  1533 
"B/B" "B/B" "B/B" "B/Y" "A/A" "A/Y" "B/B" "B/B" "B/B" "B/Y" "B/Y" "B/B" "B/B" 
  265   271  1289   113   611  1508  1142   300  1518  1314   697   355  1229 
   "" "A/B" "B/Y" "A/Y"    "" "B/Y" "A/B" "A/B"    "" "B/B" "B/Y" "B/B" "A/B" 
  679  1196   696   790   207  1123   622   996  1175   313   592  1615  1330 
"B/Y" "A/A" "B/Y" "B/Y" "B/B" "A/B" "A/B" "A/B" "B/B" "B/Y" "B/Y" "B/Y" "B/B" 
 1292  1353   372  1445  1724  1388   452   876  1120   218  1428  1534   515 
"A/B" "B/B" "B/B" "B/Y" "A/Y" "B/Y" "B/B" "A/Y" "B/Y" "A/Y" "B/Y"    ""    "" 
 1132   454   815   800   594  1555  1484  1789   922   981   600     1  1858 
"B/B" "A/B" "B/Y" "B/Y" "B/Y" "B/B" "B/Y" "B/B" "A/B" "B/Y" "A/Y" "A/B" "B/Y" 
 1855  1089  1756   491  1727   201   844  1907  1157  1473 
"B/B" "B/B"    "" "B/Y" "A/Y" "B/Y" "B/Y" "B/Y" "B/B" "B/Y" 

chopsticks documentation built on Nov. 8, 2020, 7:51 p.m.