Count Matrix Accessors

By default, counts() returns the raw counts. Normalized counts, including transcripts per million (TPM) can be accessed using the normalized argument.

# S4 method for bcbioRNASeq
counts(object, normalized = FALSE)

Arguments

object	Object.
normalized	Select raw counts (FALSE), DESeq2 normalized counts (TRUE), or additional normalization methods: tpm: Transcripts per million. tmm: Trimmed mean of M-values (edgeR). rlog: Regularized log transformation (DESeq2::rlog()). vst: Variance stabilizing transformation (DESeq2::varianceStabilizingTransformation()).

Value

matrix.

Examples

data(bcb)

# Raw counts
counts(bcb, normalized = FALSE) %>% summary()
#>     group1_1            group1_2           group2_1            group2_2        
#>  Min.   :     0.00   Min.   :0.00e+00   Min.   :     0.00   Min.   :     0.00  
#>  1st Qu.:     0.00   1st Qu.:0.00e+00   1st Qu.:     0.00   1st Qu.:     0.00  
#>  Median :     0.00   Median :0.00e+00   Median :     0.00   Median :     0.00  
#>  Mean   :   573.33   Mean   :1.02e+03   Mean   :   978.47   Mean   :  1114.48  
#>  3rd Qu.:     7.99   3rd Qu.:7.96e+00   3rd Qu.:     9.21   3rd Qu.:     8.02  
#>  Max.   :125708.15   Max.   :1.70e+05   Max.   :172785.31   Max.   :182449.79  

# TPM
counts(bcb, normalized = "tpm") %>% summary()
#>     group1_1            group1_2            group2_1        
#>  Min.   :    0.000   Min.   :    0.000   Min.   :    0.000  
#>  1st Qu.:    0.000   1st Qu.:    0.000   1st Qu.:    0.000  
#>  Median :    0.000   Median :    0.000   Median :    0.000  
#>  Mean   :   53.072   Mean   :   72.537   Mean   :   76.475  
#>  3rd Qu.:    0.186   3rd Qu.:    0.149   3rd Qu.:    0.177  
#>  Max.   :14419.300   Max.   :15656.400   Max.   :16853.700  
#>     group2_2        
#>  Min.   :    0.000  
#>  1st Qu.:    0.000  
#>  Median :    0.000  
#>  Mean   :   86.122  
#>  3rd Qu.:    0.184  
#>  Max.   :17995.900  

# DESeq2 normalized counts
# NOT RUN {
counts(bcb, normalized = TRUE)
# }

# rlog
# NOT RUN {
counts(bcb, normalized = "rlog")
# }

# TMM
# NOT RUN {
counts(bcb, normalized = "tmm")
# }

# VST
# NOT RUN {
counts(bcb, normalized = "vst")
# }