test.dat.counts


An example, a data frame of reads counts of testing samples


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)

test.dat.counts function

A data frame with 1527 observations on the following 6 variables.
  <dl>
    <dt><code>gene</code></dt><dd>a factor with levels <code>ERCC-00002</code> <code>ERCC-00003</code> <code>ERCC-00007</code> <code>ERCC-00009</code> <code>ERCC-00012</code> <code>ERCC-00013</code> <code>ERCC-00014</code> <code>ERCC-00016</code> <code>ERCC-00017</code> <code>ERCC-00018</code> <code>ERCC-00019</code> <code>ERCC-00022</code> <code>ERCC-00023</code> <code>ERCC-00024</code> <code>ERCC-00025</code> <code>ERCC-00028</code> <code>ERCC-00031</code> <code>ERCC-00033</code> <code>ERCC-00034</code> <code>ERCC-00035</code> <code>ERCC-00039</code> <code>ERCC-00040</code> <code>ERCC-00041</code> <code>ERCC-00042</code> <code>ERCC-00044</code> <code>ERCC-00048</code> <code>ERCC-00054</code> <code>ERCC-00057</code> <code>ERCC-00058</code> <code>ERCC-00059</code> <code>ERCC-00061</code> <code>ERCC-00079</code> <code>ERCC-00084</code> <code>ERCC-00170</code></dd> <dt><code>pos</code></dt><dd>a numeric vector</dd> <dt><code>code_strand</code></dt><dd>a factor with levels <code>+</code></dd> <dt><code>seq_strand</code></dt><dd>a factor with levels <code>S</code></dd> <dt><code>GSM516589_run32_s_2_ERCC_map_Pos</code></dt><dd>a numeric vector</dd> <dt><code>GSM517059_run29_s_1_ERCC_map_Pos</code></dt><dd>a numeric vector</dd> </dl> 

test.dat.counts: Testing Counts Dataset

Description

Usage

Arguments

Format

References

Examples