ISoLDE (version 1.0.2)

normASRcounts: 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.

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).

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.

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)