Merges individual CAGE samples (datasets, experiments) within the CAGEr object into specified groups.
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Integer vector specifying which experiments should be merged. (one value per sample, see Details).
Labels for the merged datasets (same length as the
number of unique values in
The samples within the CAGEr object are merged by adding the raw tag counts of individual CTSS that belong tho the same group. After merging, all other slots in the CAGEr object will be reset and any previous data for individual experiments will be removed.
mergeIndex controls which samples will be merged. It is an integer
vector that assigns a group identifier to each sample, in the same order as
they are returned by
sampleLabels(object). For example, if there are
8 CAGE samples in the CAGEr object and
mergeIndex = c(1,1,2,2,3,2,4,4),
this will merge a) samples 1 and 2, b) samples 3, 4 and 6, c) samples 7 and
8, and d) it will leave sample 5 as it is, resulting in 4 final merged datasets.
Labels provided in
mergedSampleLabels will be assigned to merged datasets in the ascending
mergeIndex values, i.e. first label will be assigned to a dataset created
by merging datasets labeled with lowest
mergeIndex value (in this case
tagCountMatrix of the
CAGEr object will be updated with the information on merged CAGE datasets
and will replace the previous information on individual CAGE datasets. All further slots with
downstream information will be reset.
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