load_BAM: Load .BAM file into R as tibble
In JakobPedersenLab/dreams: Deep Read-level Error Model for Sequencing data
load_BAM R Documentation
Load .BAM file into R as tibble
Description
This function reads alignment data from a .BAM file and formats it as a tibble (data frame) in R.
It allows for the selection of specific genomic regions by specifying chromosomes and positions, and it extracts
relevant alignment data including tags for further analysis. The function also includes processing of UMI tags
and correction for hard clips in the CIGAR strings.
Usage
load_BAM(BamPath, chr = NULL, pos = NULL)
Arguments
BamPath
The file path to the .BAM file to be loaded.
chr
A vector of chromosome identifiers indicating the chromosomes of interest for the analysis. (strings)
pos
A vector of numeric positions indicating the specific locations of interest within the chromosomes. (numeric)
Value
A tibble (data frame) containing the extracted alignment data from the .BAM file, including processed UMI
features and genomic positions, as well as any necessary corrections for alignment issues such as hard clipping.
JakobPedersenLab/dreams documentation built on Feb. 2, 2024, 3:14 p.m.
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| load_BAM | R Documentation |
Load .BAM file into R as tibble
Description
This function reads alignment data from a .BAM file and formats it as a tibble (data frame) in R. It allows for the selection of specific genomic regions by specifying chromosomes and positions, and it extracts relevant alignment data including tags for further analysis. The function also includes processing of UMI tags and correction for hard clips in the CIGAR strings.
Usage
load_BAM(BamPath, chr = NULL, pos = NULL)
Arguments
BamPath |
The file path to the .BAM file to be loaded. |
chr |
A vector of chromosome identifiers indicating the chromosomes of interest for the analysis. (strings) |
pos |
A vector of numeric positions indicating the specific locations of interest within the chromosomes. (numeric) |
Value
A tibble (data frame) containing the extracted alignment data from the .BAM file, including processed UMI features and genomic positions, as well as any necessary corrections for alignment issues such as hard clipping.
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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