Description Usage Arguments Details See Also Examples
This function ties together all the basics of the COMPOSE package to give you a one-stop shop for processing data.
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counts = NULL,
metadata = NULL,
sample.id = "SampleID",
save.plot = T,
save.table = T,
identifier1 = NULL,
identifier2 = NULL,
identifier3 = NULL,
batch = F,
batch.id = NULL,
transform = T,
cpm = T,
thresh = 1,
minsample.ids = 2,
meta.idnum = NULL,
cutoff = 0.5,
sig.cutoff = 0.05,
verbose = T,
top.labels = 30,
neg.controls = NULL,
essential.genes = NULL,
split = "_",
list.return = T,
pathway.analysis = F,
gene.db = NULL
)
|
counts |
input matrix containing normalized gRNA counts with gRNA ids as row names |
metadata |
input dataframe containing sample names and other identifiers or data including batch, treatments, etc. |
sample.id |
string identifying column name in metadata containing sample IDs |
save.plot |
logical - save the plot to pdf or print to screen (default saves everything to one pdf) |
save.table |
logical - save the tables (default saves everything) |
identifier1 |
string identifying column name of metadata with which to adjust color in PCA plot |
identifier2 |
string identifying column name of metadata with which to adjust size in PCA plot |
identifier3 |
string identifying column name of metadata with which to adjust shape in PCA plot |
batch |
logical - correct for batch effects (requires a batch.id input) |
batch.id |
numerical - column of metadata that identifies the batch effect to remove |
transform |
logical - do you want to log10 transform the counts |
cpm |
logical - do you want to normalize the counts by sequencing depth |
thresh |
numerical cutoff for low counts |
minsample.ids |
minimum number of samples for which counts must be present per gene |
meta.idnum |
vector containing the column numbers in metadata that represent (1) Cell line, (2) replicates, and (3) condition |
cutoff |
gene score cutoff for comparisons between contrasts (default = 1) |
sig.cutoff |
numeric - specified p-value cut-off |
verbose |
TRUE/FALSE (default = TRUE) |
top.labels |
numerical - number of top guides to label (by p-value) |
neg.controls |
input vector containing gRNA ids for negative controls |
essential.genes |
input vector containing gRNA ids for essential genes |
split |
defines the regex used to split the guide RNA id to extract the gene name |
list.return |
logical - return a list containing gene names for every intersection |
pathway.analysis |
(TRUE/FALSE) continue with pathway analysis for all contrasts |
gene.db |
genome database from which to convert gene symbols to other ids |
The required arguments to run the simplest analysis include counts, metadata, meta.idnum, essential.genes, and neg.controls (if pathway.analysis = F).
COMPOSE
the COMPOSE package
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