obj.index


Index S3 class contains two objects:  a 2-dimension matrix with nucleotides as row names and positions as column names and a flatted one with 1-dimension combinations of nucleotides and positions.


datasets

Many inherited biases and effects exists in RNA-seq due to both biological and technical effects. We observed the biological variance of testing target transcripts can influence the yield of sequencing reads, which might indicate a resource competition existing in RNA-seq. We developed this package to capture the bias depending on local sequence and perform the correction of this type of bias by borrowing information from spike-in measurement.

Guoshuai Cai

GCAI.bias

Guided Correction Approach for Inherited bias (GCAI.bias)

obj.index function

The format is: List of 2 $ mat : num [1:4, 1:81] 0 0 0 0 0 0 0 0 0 0 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:4] "A" "T" "C" "G" .. ..$ : chr [1:81] "-40" "-39" "-38" "-37" ... $ flat: chr [1:324, 1:3] "1" "2" "3" "4" ...

obj.index: Index S3 Class

Description

Usage

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Format

References

Examples