rawASRcounts: RAW ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH...
In ChristelleReynes/ISoLDE: Integrative Statistics of alleLe Dependent Expression

Description Format Details Note Source References See Also Examples

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.

rawASRcounts_file.txt: A tab-delimited file.
rawASRcounts.rda: A data.frame.

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.

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).

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).

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

readRawInput example of which uses the rawASRcounts file.

# 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)