Counts

Count matrix.

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

Arguments

object

Object.

normalized

character(1) or logical(1). Normalization method to apply: FALSE: Raw counts. When using a tximport-compatible caller, these are length scaled by default (see countsFromAbundance argument). When using a featureCounts-compatible caller, these are integer. tximport caller-specific normalizations: "tpm": Transcripts per million. Additional gene-level-specific normalizations: TRUE / "sf": Size factor (i.e. library size) normalized counts. See DESeq2::sizeFactors() for details. "fpkm": Fragments per kilobase per million mapped fragments. Requires fpkm = TRUE in bcbioRNASeq() call and gene annotations in rowRanges() with defined width. See DESeq2::fpkm() for details. "vst": Variance-stabilizing transformation (log2). Requires vst = TRUE to be set during bcbioRNASeq() call. See DESeq2::varianceStabilizingTransformation for more information. "rlog": Regularized log transformation (log2). Requires rlog = TRUE to be set during bcbioRNASeq() call. See DESeq2::rlog() for details. "tmm": Trimmed mean of M-values. Calculated on the fly. See edgeR::calcNormFactors() for details. "rle": Relative log expression transformation. Calculated on the fly. See relativeLogExpression() for details. Note that logical(1) support only applies to counts(). Other functions in the package require character(1) and use match.arg() internally.

Value

matrix.

Details

By default, return the raw counts. Normalized counts in a variety of formats can be accessed using the normalized argument.

Note

Updated 2019-09-15.

References

• TMM: Robinson and Oshlack (2010).

• RLE: Anders and Huber (2010).

See also

• tximport::tximport().

• DESeq2::counts().

• DESeq2::sizeFactors().

• DESeq2::varianceStabilizingTransformation().

• DESeq2::rlog().

• DESeq2::fpkm().

• edgeR::calcNormFactors().

• tmm().

• relativeLogExpression().

Examples

data(bcb)
summary(counts(bcb))
#>   control_rep1      control_rep2       control_rep3      fa_day7_rep1    
#>  Min.   :   0.00   Min.   :    0.00   Min.   :   0.00   Min.   :   0.00  
#>  1st Qu.:   0.00   1st Qu.:    0.00   1st Qu.:   0.00   1st Qu.:   0.00  
#>  Median :  12.12   Median :   14.17   Median :  10.72   Median :  33.48  
#>  Mean   : 176.59   Mean   :  602.45   Mean   : 161.05   Mean   : 294.82  
#>  3rd Qu.: 120.48   3rd Qu.:  419.69   3rd Qu.: 102.85   3rd Qu.: 302.74  
#>  Max.   :2865.68   Max.   :13680.79   Max.   :2154.71   Max.   :4227.90  
#>   fa_day7_rep2       fa_day7_rep3     
#>  Min.   :   0.000   Min.   :   0.000  
#>  1st Qu.:   0.761   1st Qu.:   0.005  
#>  Median :  30.355   Median :  27.788  
#>  Mean   : 262.722   Mean   : 298.832  
#>  3rd Qu.: 238.995   3rd Qu.: 215.032  
#>  Max.   :5004.905   Max.   :4540.914