BridgeRNormalizationFactors {bridger2} | R Documentation |
Calculate normalization factors for BRIC-seq datasets.
Description
BridgeRNormalizationFactors
calculates the normalization factors
for BRIC-seq datasets.
Usage
BridgeRNormalizationFactors(inputFile, group = c("Control", "Knockdown"),
hour = c(0, 1, 2, 4, 8, 12), inforColumn = 4, save = T, YMin = -2,
YMax = 2, downsamplingFig = 0.2, makeFig = FALSE,
cutoffQuantile = 0.975, figOutputPrefix = "BridgeR_3_fig",
factorOutputPrefix = "BridgeR_3")
Arguments
inputFile |
The vector of tab-delimited matrix file. |
group |
The vector of group names. |
hour |
The vector of time course about BRIC-seq experiment. |
inforColumn |
The number of information columns. |
save |
Whether to save the output matrix file. |
YMin |
Y-axis min. |
YMax |
Y-axis max. |
downsamplingFig |
the factor for downsampling. |
makeFig |
Whether to save the figure of normalization factor. |
cutoffQuantile |
cutoff value of quantile. |
figOutputPrefix |
The prefix for the name of figure output. |
factorOutputPrefix |
The prefix for the name of factor output. |
Value
data.table object about normalization factors calculated by quantile method.
Examples
library(data.table)
rpkm_matrix <- data.table(gr_id = c(8, 9, 14),
symbol = c("AAAS", "AACS", "AADAT"),
accession_id = c("NM_015665", "NM_023928", "NM_182662"),
locus = c("chr12", "chr12", "chr4"),
CTRL_1_0h = c(41, 5, 5),
CTRL_1_1h = c(48, 7, 6),
CTRL_1_2h = c(56, 10, 6),
CTRL_1_4h = c(87, 12, 10),
CTRL_1_8h = c(124, 20, 11),
CTRL_1_12h = c(185, 22, 15),
gr_id = c(8, 9, 14),
symbol = c("AAAS", "AACS", "AADAT"),
accession_id = c("NM_015665", "NM_023928", "NM_182662"),
locus = c("chr12", "chr12", "chr4"),
KD_1_0h = c(21, 10, 3),
KD_1_1h = c(33, 11, 3),
KD_1_2h = c(42, 15, 4),
KD_1_4h = c(60, 20, 5),
KD_1_8h = c(65, 37, 6),
KD_1_12h = c(70, 42, 6))
group <- c("Control", "Knockdown")
hour <- c(0, 1, 2, 4, 8, 12)
rpkm_list <- BridgeRDataSetFromMatrix(inputFile = rpkm_matrix,
group = group,
hour = hour,
cutoff = 0.1,
inforColumn = 4,
save = FALSE)
raw_table <- rpkm_list[[1]]
test_table <- rpkm_list[[2]]
factor_table <- BridgeRNormalizationFactors(test_table,
save = FALSE)
[Package bridger2 version 0.1.0 Index]