scan_spike_counts: run spike_counts on BAM/CRAM files and shape the results for...
In trichelab/spiky: Spike-in calibration for cell-free MeDIP
View source: R/scan_spike_counts.R
scan_spike_counts R Documentation
run spike_counts on BAM/CRAM files and shape the results for model_glm_pmol
Description
Typically one will want to fit a correction model to multiple samples.
This function eases this task by merging the output of spike_counts into
a data.frame that model_glm_pmol can directly fit.
Usage
scan_spike_counts(files, spike, methylated = 1, sep = "_")
Arguments
files
a vector of BAM/CRAM file names
spike
a spike-in database
methylated
a logical (0/1) to include only methylated fragments
sep
the separator for spike-in contig names ("_")
Value
a data.frame with columns "frag_grp", "id", and "read_count"
Examples
data(spike)
library(GenomicRanges)
sb <- system.file("extdata", "example.spike.bam", package="spiky",
mustWork=TRUE)
scan_spike_counts(sb, spike=spike)
fit <- model_glm_pmol(scan_spike_counts(sb, spike=spike),spike=spike)
trichelab/spiky documentation built on Sept. 17, 2022, 8:44 a.m.
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View source: R/scan_spike_counts.R
| scan_spike_counts | R Documentation |
run spike_counts on BAM/CRAM files and shape the results for model_glm_pmol
Description
Typically one will want to fit a correction model to multiple samples. This function eases this task by merging the output of spike_counts into a data.frame that model_glm_pmol can directly fit.
Usage
scan_spike_counts(files, spike, methylated = 1, sep = "_")
Arguments
files |
a vector of BAM/CRAM file names |
spike |
a spike-in database |
methylated |
a logical (0/1) to include only methylated fragments |
sep |
the separator for spike-in contig names ("_") |
Value
a data.frame with columns "frag_grp", "id", and "read_count"
Examples
data(spike)
library(GenomicRanges)
sb <- system.file("extdata", "example.spike.bam", package="spiky",
mustWork=TRUE)
scan_spike_counts(sb, spike=spike)
fit <- model_glm_pmol(scan_spike_counts(sb, spike=spike),spike=spike)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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