methylation_specificity generates NaN/NA

Hi, I am working with the following commands:

res <- scan_spiked_bam(sb, bins=GRanges())

This works fine for me:

GRangesList object of length 2:
$genomic
GRanges object with 0 ranges and 1 metadata column:
   seqnames    ranges strand |  coverage
      <Rle> <IRanges>  <Rle> | <numeric>
  -------
  seqinfo: 52 sequences from spike genome

$spikes
GRanges object with 52 ranges and 1 metadata column:
                             seqnames    ranges strand |  coverage
                                <Rle> <IRanges>  <Rle> | <numeric>
   80b_1C_35G-1          80b_1C_35G-1      1-80      * |         2
   80b_1C_35G-2 80b_1C_35G-2_mod_meth      1-80      * |        16
   80b_1C_50G-1          80b_1C_50G-1      1-80      * |         6
   80b_1C_50G-2 80b_1C_50G-2_mod_meth      1-80      * |       496
   80b_1C_65G-1          80b_1C_65G-1      1-80      * |        16
            ...                   ...       ...    ... .       ...
  320b_8C_35G-2         320b_8C_35G-2     1-320      * |         0
  320b_8C_50G-1         320b_8C_50G-1     1-320      * |         3
  320b_8C_50G-2    320b_8C_50G-2_meth     1-320      * |      1514
  320b_8C_65G-1    320b_8C_65G-1_meth     1-320      * |       407
  320b_8C_65G-2         320b_8C_65G-2     1-320      * |         3
  -------
  seqinfo: 52 sequences from spike genome

Next, when I run the following: methylation_specificity(res) I get NaNs

$mean
[1] NaN
$median
[1] NA

For the same bam file; scan_methylation_specificity works just right.

This is odd -- using the current codebase and the examples as written,

library(GenomicRanges)
sb <- system.file("extdata", "example.spike.bam", package="spiky", mustWork=TRUE)
res <- scan_spiked_bam(sb, bins=GRanges())

I get

methylation_specificity(res)
# $mean
# [1] 0.979735175
#
# $median
# [1] 0.997228632

and

scan_methylation_specificity(sb, spike=spike)
#                      mean      median
# example.spike 0.979913763 0.995485836

Granted this is with a recent push, but neither of the above functions are among the changes:

packageVersion("spiky")
# [1] '0.99.37'
R.version
#               _
# platform       x86_64-pc-linux-gnu
# arch           x86_64
# os             linux-gnu
# system         x86_64, linux-gnu
# status
# major          4
# minor          0.0
# year           2020
# month          04
# day            24
# svn rev        78286
# language       R
# version.string R version 4.0.0 (2020-04-24)
# nickname       Arbor Day

Can you post your sessionInfo() or any other information that may reveal the source of the issue?

Timothy J. Triche, Jr., PhD Assistant Professor of Bioinformatics, Van Andel Institute 330 Bostwick Avenue NE, Grand Rapids, MI, 49503 (616) 234-5316 (office) (626) 375-9663 (mobile) (616) 234-5252 (administrative, courtesy of Lauren Dunkelberg) https://trichelab.vai.org/

From: Prisni R @.***> Sent: Monday, April 5, 2021 5:17 PM To: trichelab/spiky Cc: Subscribed Subject: [External] [trichelab/spiky] methylation_specificity generates NaN/NA (#26)

Hi, I am working with the following commands: res <- scan_spiked_bam(sb, bins=GRanges()) works fine `GRangesList object of length 2: $genomic GRanges object with 0 ranges and 1 metadata column: seqnames ranges strand	coverage

seqinfo: 52 sequences from spike genome

$spikes GRanges object with 52 ranges and 1 metadata column: seqnames ranges strand	coverage
80b_1C_35G-1 80b_1C_35G-1 1-80 *	2
80b_1C_35G-2 80b_1C_35G-2_mod_meth 1-80 *	16
80b_1C_50G-1 80b_1C_50G-1 1-80 *	6
80b_1C_50G-2 80b_1C_50G-2_mod_meth 1-80 *	496
80b_1C_65G-1 80b_1C_65G-1 1-80 *	16

seqinfo: 52 sequences from spike genome`

Next, when I run the following: methylation_specificity(res) I get NaNs

$mean [1] NaN $median [1] NA

For the same bam file; scan_methylation_specificity works just right.

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trichelab / spiky

methylation_specificity generates NaN/NA #26