I was testing the package and run into some conflicts:
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When loading the file.bam, file.bai was not recognized but file.bam.bai was. According to the documentation, both types should have been recognized.
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Including padding_size throws the error Some regions are outside max chromosome length and can't be used.
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When plotting separate replicates or add a design to indicate them together, values seem to be summed (each file was ~25 and combined ~50). Is there an option to get the mean?
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I was trying to extract gene counts to replicate the division by expression level shown in the paper. As regions, I used gene features from a gff and transformed into a GRanges object. But when I use get coverage or get counts in metagene, no gene names are present to have a counts table linking each region name to the counts as calculated by metagene.
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I called the object used for regions my_genes (a GRanges object with genes from a gff transformed to txdb), but the plot added "_regions" on the group labels. Is there an option in metagene for this suffix be removed from the labels? Or be customized? i.e., on one experiment to show the labels from two columns on the samples (s1, s2), and in another to show the regions from a single sample (r1, r2, r3), instead of (s1_r1, s1_r2, s1_r3). So far, I'd just think about hard-coding with ggplot.
Cheers
I was testing the package and run into some conflicts:
When loading the
file.bam,file.baiwas not recognized butfile.bam.baiwas. According to the documentation, both types should have been recognized.Including
padding_sizethrows the errorSome regions are outside max chromosome lengthand can't be used.When plotting separate replicates or add a design to indicate them together, values seem to be summed (each file was ~25 and combined ~50). Is there an option to get the mean?
I was trying to extract gene counts to replicate the division by expression level shown in the paper. As regions, I used gene features from a gff and transformed into a GRanges object. But when I use
get coverageorget countsin metagene, no gene names are present to have a counts table linking each region name to the counts as calculated by metagene.I called the object used for regions
my_genes(a GRanges object with genes from a gff transformed to txdb), but the plot added "_regions" on the group labels. Is there an option in metagene for this suffix be removed from the labels? Or be customized? i.e., on one experiment to show the labels from two columns on the samples (s1, s2), and in another to show the regions from a single sample (r1, r2, r3), instead of (s1_r1, s1_r2, s1_r3). So far, I'd just think about hard-coding with ggplot.Cheers