qc_analysis: Run qc pipeline
In pcahan1/CellNet: Assess and improve cell fate engineering with network biology
qc_analysis R Documentation
Run qc pipeline
Description
subsamples reads, aligns to each genome, and counts the reads mapping to features in the target genome
Usage
qc_analysis(sampTab, sname = "sra_id", subProp = 0.001,
target = "mouse",
gtfFile = "/media/ephemeral1/dat/ref/Mus_musculus.GRCm38.83.gtf",
cname = "trimNames")
Arguments
sampTab
sample table
sname
column of default prefix
subProp
fraction of reads to sample
target
species/genome
gtfFile
gtf path/filename
cname
column name containing input file names
Value
sample tablein which qc measures have been appended
pcahan1/CellNet documentation built on May 18, 2023, 4:58 p.m.
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| qc_analysis | R Documentation |
Run qc pipeline
Description
subsamples reads, aligns to each genome, and counts the reads mapping to features in the target genome
Usage
qc_analysis(sampTab, sname = "sra_id", subProp = 0.001,
target = "mouse",
gtfFile = "/media/ephemeral1/dat/ref/Mus_musculus.GRCm38.83.gtf",
cname = "trimNames")
Arguments
sampTab |
sample table |
sname |
column of default prefix |
subProp |
fraction of reads to sample |
target |
species/genome |
gtfFile |
gtf path/filename |
cname |
column name containing input file names |
Value
sample tablein which qc measures have been appended
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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