normFreqRPKM: normFreqRPKM
In eprifti/momr: Mining Metaomics Data (MetaOMineR)
normFreqRPKM R Documentation
normFreqRPKM
Description
converts a raw count matrix onto a frequency matrix using the RPKM normalization method.
This method consists of two consecutive steps, first dividing the raw counts by the length of
the gene sequence and the second shrinking the signal per column to a sum of 1.
Usage
normFreqRPKM(dat, cat = NULL, HQ_reads = NULL)
Arguments
dat
: raw counts data matrix with gene_ids as rownames
cat
: the current working catalogue where the reads are mapped and counted, (i.e. hs_3.3_metahit, hs_3.9_metahit)
This can also be a vector of genelength values that correspond to the number of rows in the dat matrix and are
ordered respectively
HQ_reads
: To take into account a vector of high quality reads that are not mapped.
Details
normFreqRPKM
Value
a normalized frequency matrix
Author(s)
Edi Prifti & Emmanuelle Le Chatelier
eprifti/momr documentation built on Dec. 11, 2024, 3:06 p.m.
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.
| normFreqRPKM | R Documentation |
normFreqRPKM
Description
converts a raw count matrix onto a frequency matrix using the RPKM normalization method. This method consists of two consecutive steps, first dividing the raw counts by the length of the gene sequence and the second shrinking the signal per column to a sum of 1.
Usage
normFreqRPKM(dat, cat = NULL, HQ_reads = NULL)
Arguments
dat |
: raw counts data matrix with gene_ids as rownames |
cat |
: the current working catalogue where the reads are mapped and counted, (i.e. hs_3.3_metahit, hs_3.9_metahit) This can also be a vector of genelength values that correspond to the number of rows in the dat matrix and are ordered respectively |
HQ_reads |
: To take into account a vector of high quality reads that are not mapped. |
Details
normFreqRPKM
Value
a normalized frequency matrix
Author(s)
Edi Prifti & Emmanuelle Le Chatelier
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.