ISoLDE (version 1.0.2)

rawASRcounts: RAW ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES

Description

rawASRcounts_file.txt: A tab-delimited text file containing the raw values of ASR counts for an experiment with more than two replicates. rawASRcounts.rda: the rawASRcounts_file.txt loaded into a data.frame by the readRawInput function.

Format

rawASRcounts_file.txt: A tab-delimited file. rawASRcounts.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 raw allele-specific read counts. In case of double input, columns must be in the same order in both raw and normalized ASR counts files. The rawASRcounts_file.txt file should be read and checked by the readRawInput 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

readRawInput example of which uses the rawASRcounts file.

Examples

# rawASRcounts_file.txt
rawfile <- system.file("extdata", "rawASRcounts_file.txt", 
package = "ISoLDE")
rawASRcounts <- readRawInput(raw_file = rawfile, del = "tab", 
colnames = TRUE, rownames = TRUE)

# rawASRcounts.rda
data(rawASRcounts)