bic.format.htseq.counts: Read in raw HTSeq count file and format for analysis
In bic-mskcc/bicrnaseq: MSKCC Bioinformatics Core RNASeq
Description
Usage
Arguments
Value
Description
Reformatting includes removing samples that are not in
sample key (if key is provided), rounding counts to
nearest integer, assigning GeneIDs to rownames of matrix,
and removing GeneID column from matrix if it also contains
a GeneSymbol column.
Usage
1
bic.format.htseq.counts(htseq.file, key = NULL)
Arguments
htseq.file
tab-delimited file containing raw HTseq
counts; columns are samples and rows are
genes; must contain GeneID column but may
also contain a GeneSymbol column
key
two-column matrix where column one contains
all samples to be included in analysis and
column two contains condition groups to which
the samples belong
Value
a list of two items: 1) a matrix of raw counts formatted
for BIC differential expression analysis and 2) a vector
of gene symbols named by the GeneID in htseq file (this
vector will be NULL if there is no GeneSymbol column in
the htseq file.
bic-mskcc/bicrnaseq documentation built on May 24, 2019, 3:04 a.m.
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Description Usage Arguments Value
Description
Reformatting includes removing samples that are not in sample key (if key is provided), rounding counts to nearest integer, assigning GeneIDs to rownames of matrix, and removing GeneID column from matrix if it also contains a GeneSymbol column.
Usage
1 | bic.format.htseq.counts(htseq.file, key = NULL)
|
Arguments
htseq.file |
tab-delimited file containing raw HTseq counts; columns are samples and rows are genes; must contain GeneID column but may also contain a GeneSymbol column |
key |
two-column matrix where column one contains all samples to be included in analysis and column two contains condition groups to which the samples belong |
Value
a list of two items: 1) a matrix of raw counts formatted for BIC differential expression analysis and 2) a vector of gene symbols named by the GeneID in htseq file (this vector will be NULL if there is no GeneSymbol column in the htseq file.
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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