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Showing content from https://github.com/stuart-lab/signac/issues/12 below:

10X sample alignment · Issue #12 · stuart-lab/signac · GitHub

I'm trying to align 2 10X datasets that should be very similar.
sci <- brain03
tenx <- brain

At this code, I get an error unless I change the code to the following:

intersecting.regions <- GetIntersectingFeatures(
object.1 = sci,
object.2 = tenx,
sep.1 = c(":", "-"), ## from c("-", "-")
sep.2 = c(":", "-")
)

The error reads as follows:

Error in .get_data_frame_col_as_numeric(df, granges_cols[["end"]]) :
some values in the "end" column cannot be turned into numeric values
In addition: Warning message:
Expected 3 pieces. Missing pieces filled with NA in 96883 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

By changing the hypen to a colon I can get past that but then I get the following error running this code:

sci_peaks_tenx <- FeatureMatrix(
fragments = GetFragments(object = tenx, assay = 'peaks'),
features = StringToGRanges(peaks.use),
cells = colnames(tenx)
)
Error in .get_data_frame_col_as_numeric(df, granges_cols[["end"]]) :
some values in the "end" column cannot be turned into numeric values
In addition: Warning message:
Expected 3 pieces. Missing pieces filled with NA in 10000 rows [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].

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