normASRcounts {ISoLDE} | R Documentation

## NORMALIZED ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES

### Description

normASRcounts_file.txt: A tab-delimited text file containing the normalized values of ASR counts for an experiment with more than two replicates.
normASRcounts.rda: the normASRcounts_file.txt loaded into a data.frame by the
`readNormInput` function.

### Format

normASRcounts_file.txt: A tab-delimited file.
normASRcounts.rda: A data.frame.

### Details

Each line represents a feature (e.g. a gene or a transcript).
Each column represents the number of allele-specific sens reads from either
the paternal or maternal parent for a given biological replicate, so that
you expect to have two columns per biological replicate.
Values in the matrix are normalized (RLE method) ASR counts.
In case of double input, columns must be in the same order in both raw and normalized ASR counts files.
The normASRcounts_file.txt file should be read and checked by the `readNormInput` function.

### Note

A minimum of two biological replicates per cross is mandatory, however, we strongly recommend to use more than two replicates per cross. This enables a better estimation of variability and to use the bootstrap method to perform the statistical test (see the `isolde_test` function).

### Source

Extract from Bouschet, T. et al. (2016): In vitro corticogenesis from embryonic stem cells recapitulates the in vivo epigenetic control of imprinted gene expression. Submitted Subset of 6062 genes (after filtering).

### References

Bouschet, T. et al. (2016): In vitro corticogenesis from embryonic stem cells recapitulates the in vivo epigenetic control of imprinted gene expression. Submitted

### See Also

`readNormInput` example of which uses the `normASRcounts` file.

### Examples

    # normASRcounts_file.txt
    normfile <- system.file("extdata", "normASRcounts_file.txt",
    package = "ISoLDE")
    normASRcounts <- readNormInput(norm_file = normfile, del = "tab",
    rownames = TRUE, colnames = TRUE)

    # normASRcounts.rda
    data(normASRcounts)

[Package ISoLDE version 1.12.0 Index]