Description Usage Arguments Value See Also Examples
Compute frequencies or counts of gene segments ("V / J - usage").
1 2 3 4 5 6 7 | geneUsage(
.data,
.genes = HUMAN_TRBV_MITCR,
.quant = c(NA, "read.count", "umi.count", "read.prop", "umi.prop"),
.norm = F,
.ambig = F
)
|
.data |
Cloneset data frame or a list with clonesets. |
.genes |
Either one of the gene alphabet (e.g., HUMAN_TRBV, genealphabets) or list with two gene alphabets for computing joint distribution. |
.quant |
Which column to use for the quantity of clonotypes: NA for computing only number of genes without using clonotype counts, "read.count" for the "Read.count" column, "umi.count" for the "Umi.count" column, "read.prop" for the "Read.proportion" column, "umi.prop" for the "Umi.proportion" column. |
.norm |
If T then return proportions of resulting counting of genes. |
.ambig |
If F than remove from counting genes which are not presented in the given gene alphabet(s). |
If .data
is a cloneset and .genes
is NOT a list than return a data frame with first column "Gene" with genes and second with counts / proportions.
If .data
is a list with clonesets and .genes
is NOT a list than return a data frame with first column "Gene"
with genes and other columns with counts / proportions for each cloneset in the input list.
If .data
is a cloneset and .genes
IS a list than return a matrix with gene segments for the first gene in .genes
and column names for the second gene in .genes
. See "Examples".
If .data
is a list with clonesets and .genes
IS a list than return a list with matrices like in the previous case.
genealphabets
, vis.gene.usage
, pca.segments
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Not run:
# Load your data
data(twb)
# compute V-segments frequencies of human TCR beta.
seg <- geneUsage(twb, HUMAN_TRBV, .norm = T)
# plot V-segments frequencies as a heatmap
vis.heatmap(seg, .labs = c("Sample", "V gene"))
# plot V-segments frequencies directly from clonesets
vis.gene.usage(twb, HUMAN_TRBV)
# plot V-segments frequencies from the gene frequencies
vis.gene.usage(seg, NA)
# Compute V-J joint usage.
geneUsage(twb, list(HUMAN_TRBV, HUMAN_TRBJ))
# for future:
# geneUsage(twb, "human", "trbv")
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.