could not find function "scanBam"
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@702b1449
Last seen 3.2 years ago
United States

After I loaded the package Rsamtools, I tried to read a ban data file. Then I got the error message

Error in scanBam("C:/Sequence/SeqData/bam/A1.bam") : could not find function "scanBam"

Here is the R code

load library

library(Rsamtools)

read in entire BAM file

bam <- scanBam("C:/Sequence/SeqData/bam/A1.bam")

Session Info as follows

sessionInfo( )

R version 4.0.5 (2021-03-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] BiocManager_1.30.15

loaded via a namespace (and not attached): [1] compiler_4.0.5 tools_4.0.5

Rsamtool Rsamtools • 1.0k views
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Entering edit mode
@martin-morgan-1513
Last seen 3 days ago
United States

Your sessionInfo() does not show Rsamtools as an 'other attached packages', so Rsamtools failed to load on your system. Perhaps there was an error that you did not show us? For instance, is Rsamtools installed via

BiocManager::install("Rsamtools")
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