SnpMatrix-class: Class "SnpMatrix"

In snpStats: SnpMatrix and XSnpMatrix classes and methods

Description

This class defines objects holding large arrays of single nucleotide polymorphism (SNP) genotypes generated using array technologies.

Objects from the Class

Objects can be created by calls of the form new("SnpMatrix", x) where x is a matrix with storage mode "raw". Chips (usually corresponding to samples or subjects) define rows of the matrix while polymorphisms (loci) define columns. Rows and columns will usually have names which can be used to link the data to further data concerning samples and SNPs

Slots

.Data:

Object of class "matrix" and storage mode raw Internally, missing data are coded 0 and SNP genotypes are coded 1, 2 or 3. Imputed values may not be known exactly. Such uncertain calls are grouped by probability and represented by codes 4 to 253

Extends

Class "matrix", from data part. Class "structure", by class "matrix". Class "array", by class "matrix". Class "vector", by class "matrix", with explicit coerce. Class "vector", by class "matrix", with explicit coerce.

Methods

[]

signature(x = "SnpMatrix", i = "ANY", j = "ANY", drop = "missing"): subset operations

cbind2

signature(x = "SnpMatrix", y = "SnpMatrix"): S4 generic function to provide cbind() for two or more matrices together by column. Row names must match and column names must not coincide. If the matrices are of the derived class XSnpMatrix-class, the diploid slot values must also agree

coerce

signature(from = "SnpMatrix", to = "numeric"): map to numeric values 0, 1, 2 or, for uncertain assignments, to the posterior expectation of the 0, 1, 2 code

coerce

signature(from = "SnpMatrix", to = "character"): map to codes "A/A", "A/B", "B/B", ""

coerce

signature(from = "matrix", to = "SnpMatrix"): maps numeric matrix (coded 0, 1, 2 or NA) to a SnpMatrix

coerce

signature(from = "SnpMatrix", to = "XSnpMatrix"): maps a SnpMatrix to an XSnpMatrix. Ploidy is inferred from the genotype data since haploid genotypes should always be coded as homozygous. After inferring ploidy, heterozygous calls for haploid genotypes are set to NA

is.na

signature(x = "SnpMatrix"): returns a logical matrix indicating whether each element is NA

rbind2

signature(x = "SnpMatrix", y = "snp.matrix"): S4 generic function to provide rbind() for two or more matrices by row. Column names must match and duplicated row names prompt warnings

show

signature(object = "SnpMatrix"): shows the size of the matrix (since most objects will be too large to show in full)

summary

signature(object = "SnpMatrix"): returns summaries of the data frames returned by row.summary and col.summary

is.na

signature(x = "SnpMatrix"): returns a logical matrix of missing call indicators

switch.alleles

signature(x = "SnpMatrix", snps ="ANY"): Recode specified columns of of the matrix to reflect allele switches

Note

This class requires at least version 2.3 of R

Author(s)

David Clayton [e-mail]

See Also

XSnpMatrix-class

Examples

data(testdata)
summary(Autosomes)

# Just making it up - 3-10 will be made into NA during conversion
snps.class<-new("SnpMatrix", matrix(1:10))
snps.class
if(!isS4(snps.class)) stop("constructor is not working")

pretend.X <- as(Autosomes, 'XSnpMatrix')
if(!isS4(pretend.X)) stop("coersion to derived class is not S4")
if(class(pretend.X) != 'XSnpMatrix') stop("coersion to derived class is not working")

pretend.A <- as(Xchromosome, 'SnpMatrix')
if(!isS4(pretend.A)) stop("coersion to base class is not S4")
if(class(pretend.A) != 'SnpMatrix') stop("coersion to base class is not working")

# display the first 10 snps of the first 10 samples
print(as(Autosomes[1:10,1:10], 'character'))

# convert the empty strings (no-calls) explicitly to "NC" before
# writing to an (anonymous and temporary) csv file
csvfile <- tempfile()
write.csv(file=csvfile, gsub ('^$', 'NC',
                              as(Autosomes[1:10,1:10], 'character')
                             ), quote=FALSE)
unlink(csvfile)

Example output

Loading required package: survival
Loading required package: Matrix
$rows
   Call.rate      Certain.calls Heterozygosity  
 Min.   :0.6577   Min.   :1     Min.   :0.2182  
 1st Qu.:0.6963   1st Qu.:1     1st Qu.:0.2550  
 Median :0.9455   Median :1     Median :0.2599  
 Mean   :0.8657   Mean   :1     Mean   :0.2598  
 3rd Qu.:0.9628   3rd Qu.:1     3rd Qu.:0.2642  
 Max.   :0.9781   Max.   :1     Max.   :0.2820  

$cols
     Calls         Call.rate      Certain.calls      RAF        
 Min.   :  0.0   Min.   :0.0000   Min.   :1     Min.   :0.0000  
 1st Qu.:265.0   1st Qu.:0.6625   1st Qu.:1     1st Qu.:0.1610  
 Median :394.0   Median :0.9850   Median :1     Median :0.4775  
 Mean   :346.3   Mean   :0.8657   Mean   :1     Mean   :0.4882  
 3rd Qu.:398.0   3rd Qu.:0.9950   3rd Qu.:1     3rd Qu.:0.8166  
 Max.   :400.0   Max.   :1.0000   Max.   :1     Max.   :1.0000  
                                  NA's   :43    NA's   :43      
      MAF              P.AA              P.AB              P.BB        
 Min.   :0.0000   Min.   :0.00000   Min.   :0.00000   Min.   :0.00000  
 1st Qu.:0.0325   1st Qu.:0.03275   1st Qu.:0.06172   1st Qu.:0.02506  
 Median :0.1713   Median :0.26984   Median :0.28444   Median :0.22822  
 Mean   :0.1920   Mean   :0.38189   Mean   :0.25975   Mean   :0.35836  
 3rd Qu.:0.3289   3rd Qu.:0.70551   3rd Qu.:0.43609   3rd Qu.:0.66582  
 Max.   :0.5000   Max.   :1.00000   Max.   :1.00000   Max.   :1.00000  
 NA's   :43       NA's   :43        NA's   :43        NA's   :43       
     z.HWE         
 Min.   :-19.9499  
 1st Qu.: -0.5980  
 Median :  0.0754  
 Mean   : -0.0197  
 3rd Qu.:  0.6803  
 Max.   : 16.2481  
 NA's   :1254      

coercing object of mode  numeric  to SnpMatrix
object has no names - using numeric order for row/column names
A SnpMatrix with  10 rows and  1 columns
Row names:  1 ... 10 
Col name:  1 
Warning message:
In initialize(value, ...) :
  diploid slot not supplied; it has been estimated from heterozygosity
     173760 173761 173762 173767 173769 173770 173772 173774 173775 173776
1987 "A/A"  "A/A"  "A/A"  "B/B"  "B/B"  "B/B"  "B/B"  "A/B"  "A/A"  "A/A" 
436  "A/A"  "B/B"  "B/B"  "B/B"  "B/B"  "B/B"  "B/B"  "B/B"  "A/A"  "A/A" 
762  "A/A"  "A/B"  "A/B"  "A/B"  "B/B"  "B/B"  "B/B"  "A/B"  "A/A"  "A/A" 
1199 "A/A"  "A/B"  "A/B"  "A/A"  "B/B"  "B/B"  "B/B"  "B/B"  "A/A"  "A/A" 
1296 "A/A"  "A/A"  "A/A"  "A/B"  "B/B"  "B/B"  "B/B"  "B/B"  "A/A"  "A/A" 
81   "A/A"  "A/B"  "A/B"  "A/B"  "B/B"  "B/B"  "B/B"  "B/B"  "A/B"  "A/A" 
1278 "A/A"  "B/B"  "B/B"  "NA"   "B/B"  "B/B"  "B/B"  "B/B"  "B/B"  "A/A" 
1610 "A/A"  "A/A"  "A/A"  "A/B"  "A/B"  "B/B"  "B/B"  "A/B"  "A/A"  "A/A" 
1121 "A/A"  "A/A"  "A/A"  "A/A"  "B/B"  "B/B"  "B/B"  "B/B"  "A/B"  "A/B" 
1825 "A/A"  "A/B"  "A/B"  "B/B"  "B/B"  "B/B"  "B/B"  "B/B"  "A/A"  "A/A" 

snpStats documentation built on Nov. 8, 2020, 10:59 p.m.