Description Usage Arguments Value Author(s) See Also Examples
View source: R/experiment_FastQPCR.R
Fast way to deal with results of qRT-PCR,including compared plot,statistics and quality control.
1 2 3 4 5 6 7 8 | FastQPCR(data, sample = "samples", marker = "markers",
bioRepeat = "biorepeat", parallelRepeat = "parepeat",
group = "groups", group.control = "control", internal = "GAPDH",
value = "Ct", plot.type = c(1, 2)[1], palette = NULL, size = 20,
label.position = c(4, 5), label.type = c("p.signif", "p.format")[1],
method = "t.test", x.title = "Genes",
y.title = "The Relative Expression of Genes",
legend.position = "top")
|
data |
the result of qRT-PCR. |
sample |
the colnames of sample.Note that different samples should use different sample id. |
marker |
the colnames of marker |
bioRepeat |
the colnames of bioRepeat.The data in "bioRepeat" would be considered as available repeat in afterward statistics. |
parallelRepeat |
the colnames of parallelRepeat.The data in "parallelRepeat" would be treated via mean strategy. |
group |
the colnames of group.Like "treatment" and "control". |
group.control |
the names of control group.Default is "control". |
internal |
the name of internal reference gene.Default is "GAPDH". |
value |
the colnames of Ct value |
plot.type |
one of 1 and 2.1 is used in multiple markers,but 2 is more suitable for one marker. |
palette |
the color of groups.The number of color must be equal to the number of groups.Default is NULL,which mean that the strategy of lucky package would be use. |
size |
ggplot parameters.the size of plot |
label.position |
ggplot parameters.the position of p significance |
label.type |
character string specifying label type. Allowed values include "p.signif" (shows the significance levels), "p.format" (shows the formatted p value). |
method |
method use in statistics."t.test" is always recommended.You can also use "wilcox.test" for a try.Alternative choices are "anova" and "kruskal.test". |
x.title |
ggplot parameters.the x axis title |
y.title |
ggplot parameters.the y axis title |
legend.position |
ggplot parameters.legend position |
a Lucky Objects
Weibin Huang<654751191@qq.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | library(lucky)
data("qpcr",package = "lucky") # see the example of qpcr result
result.pcr <- FastQPCR(qpcr)
result.pcr <- FastQPCR(data=qpcr,
sample = "samples",
marker = "markers",
bioRepeat = "biorepeat",
parallelRepeat = "parepeat",
group = "groups",
group.control = "control",
internal = "GAPDH",
value = "Ct",
size=20,
label.y = 650,
method = "t.test",
x.title = "Genes",
y.title = "The Relative Expression of Genes",
legend.position = "top")
## Use t.test.However,it's not recommand.
result.pcr <- FastQPCR(data=qpcr,
sample = "samples",
marker = "markers",
bioRepeat = "biorepeat",
parallelRepeat = "parepeat",
group = "groups",
group.control = "control",
internal = "GAPDH",
value = "Ct",
size=20,
label.y = 650,
method = "t.test", #t.test
x.title = "Genes",
y.title = "The Relative Expression of Genes",
legend.position = "top")
## View result
View(result_qpcr$Data$statistc$whole)
View(result_qpcr$Data$statistc$pair)
## test
a = result.pcr$Data$metadata
x <- a$fc[a$markers %in% "marker1" & a$groups %in% "control"]
y <- a$fc[a$markers %in% "marker1" & a$groups %in% "treat"]
t.test(x,y)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.