R -- factor因子

factor(x = character(), levels, labels = levels,
exclude = NA, ordered = is.ordered(x), nmax = NA)

• x
  a vector of data, usually taking a small number of distinct values.

• levels
  an optional vector of the unique values (as character strings) that x might have taken. The default is the unique set of values taken by as.character(x), sorted into increasing order of x. Note that this set can be specified as smaller than sort(unique(x)).

• labels
  either an optional character vector of labels for the levels (in the same order as levels after removing those in exclude), or a character string of length 1. Duplicated values in labels can be used to map different values of x to the same factor level.

• exclude
  a vector of values to be excluded when forming the set of levels. This may be factor with the same level set as x or should be a character.

rt3 <- readRDS("/mnt/d/TCGA/TCGA_clinical_ALL.rds")

print(rt3[1:4,1:3])

           sample     _PATIENT cancer type abbreviation
1 TCGA-OR-A5J1-01 TCGA-OR-A5J1                      ACC
2 TCGA-OR-A5J2-01 TCGA-OR-A5J2                      ACC
3 TCGA-OR-A5J3-01 TCGA-OR-A5J3                      ACC
4 TCGA-OR-A5J5-01 TCGA-OR-A5J5                      ACC

unique(rt3$'cancer type abbreviation')

1. 'ACC'
2. 'BLCA'
3. 'BRCA'
4. 'CESC'
5. 'CHOL'
6. 'COAD'
7. 'DLBC'
8. 'ESCA'
9. 'GBM'
10. 'HNSC'
11. 'KICH'
12. 'KIRC'
13. 'KIRP'
14. 'LAML'
15. 'LGG'
16. 'LIHC'
17. 'LUAD'
18. 'LUSC'
19. 'MESO'
20. 'OV'
21. 'PAAD'
22. 'PCPG'
23. 'PRAD'
24. 'READ'
25. 'SARC'
26. 'SKCM'
27. 'STAD'
28. 'TGCT'
29. 'THCA'
30. 'THYM'
31. 'UCEC'
32. 'UCS'
33. 'UVM'

本来是字符型变量的

typeof(rt3$'cancer type abbreviation')

‘character’

作为因子后成为数值变量了（每个数值代表一个等级）

rt3$'cancer type abbreviation' <- factor(rt3$'cancer type abbreviation')

typeof(rt3$'cancer type abbreviation')

‘integer’

unique(rt3$'cancer type abbreviation')

1. ACC
2. BLCA
3. BRCA
4. CESC
5. CHOL
6. COAD
7. DLBC
8. ESCA
9. GBM
10. HNSC
11. KICH
12. KIRC
13. KIRP
14. LAML
15. LGG
16. LIHC
17. LUAD
18. LUSC
19. MESO
20. OV
21. PAAD
22. PCPG
23. PRAD
24. READ
25. SARC
26. SKCM
27. STAD
28. TGCT
29. THCA
30. THYM
31. UCEC
32. UCS
33. UVM

Levels:

1. 'ACC'
2. 'BLCA'
3. 'BRCA'
4. 'CESC'
5. 'CHOL'
6. 'COAD'
7. 'DLBC'
8. 'ESCA'
9. 'GBM'
10. 'HNSC'
11. 'KICH'
12. 'KIRC'
13. 'KIRP'
14. 'LAML'
15. 'LGG'
16. 'LIHC'
17. 'LUAD'
18. 'LUSC'
19. 'MESO'
20. 'OV'
21. 'PAAD'
22. 'PCPG'
23. 'PRAD'
24. 'READ'
25. 'SARC'
26. 'SKCM'
27. 'STAD'
28. 'TGCT'
29. 'THCA'
30. 'THYM'
31. 'UCEC'
32. 'UCS'
33. 'UVM'

因子将其分为了很多组，现在通过levels和labels修改分组

rt3$'cancer type abbreviation' <- factor(rt3$'cancer type abbreviation',
                                        levels=c('ACC','BLCA','BRCA','CESC','CHOL','COAD','DLBC','ESCA','GBM','HNSC','KICH','KIRC','KIRP','LAML','LGG','LIHC','LUAD','LUSC','MESO','OV','PAAD','PCPG','PRAD','READ','SARC','SKCM','STAD','TGCT','THCA','THYM','UCEC','UCS','UVM'),
                                        labels=c('ACC','BLCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA','BRCA'))

typeof(rt3$'cancer type abbreviation')

‘integer’

unique(rt3$'cancer type abbreviation')

1. ACC
2. BLCA
3. BRCA

Levels:

1. 'ACC'
2. 'BLCA'
3. 'BRCA'

factor 转化为as.numeric存在的陷阱

a <- as.numeric(rt3$'cancer type abbreviation')
unique(a)

1. 1
2. 2
3. 3

b <- factor(c(2:8),levels=c("2","3","4","5","6","7","8"),labels=c("1","2","3","4","5","6","7"))

b

1. 1
2. 2
3. 3
4. 4
5. 5
6. 6
7. 7

Levels:

1. '1'
2. '2'
3. '3'
4. '4'
5. '5'
6. '6'
7. '7'

as.numeric(b)

1. 1
2. 2
3. 3
4. 4
5. 5
6. 6
7. 7