read_coverage: Read output from my 'coverage.py' script
In andrewparkermorgan/popcorn: File-Format Wrangler for Population-Based Genetic Data
read_coverage R Documentation
Read output from my coverage.py script
Description
Read output from my coverage.py script
Usage
read_coverage(path, scrub = TRUE, as.ranges = FALSE, has.MQ0 = FALSE, ...)
Arguments
path
name of file to read
scrub
if TRUE, remove trailing suffixes (*.sorted, *.merged etc) from individual IDs
as.ranges
if TRUE, convert to a GRanges object
Details
Expected input is a BED-like file with columns *chr*, *start*, *end*, *iid*, *raw read count*,
*normalized read count* and optionally *count of MQ0 reads*, *proportion of total reads which are MQ0*.
Value
a dataframe
andrewparkermorgan/popcorn documentation built on July 8, 2023, 12:42 p.m.
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| read_coverage | R Documentation |
Read output from my coverage.py script
Description
Read output from my coverage.py script
Usage
read_coverage(path, scrub = TRUE, as.ranges = FALSE, has.MQ0 = FALSE, ...)
Arguments
path |
name of file to read |
scrub |
if |
as.ranges |
if |
Details
Expected input is a BED-like file with columns *chr*, *start*, *end*, *iid*, *raw read count*, *normalized read count* and optionally *count of MQ0 reads*, *proportion of total reads which are MQ0*.
Value
a dataframe
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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