diff --git a/DESCRIPTION b/DESCRIPTION
index 1fdc4cd..a8da22e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: msDiaLogue
Title: Analysis + Visuals for Data Indep. Aquisition Mass Spectrometry Data
-Version: 0.0.4
+Version: 0.0.5
Authors@R: c(
person("Shiying", "Xiao", email = "shiying.xiao@uconn.edu",
role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8846-3258")),
diff --git a/R/analyze.R b/R/analyze.R
index bf4dfaa..f077eb9 100644
--- a/R/analyze.R
+++ b/R/analyze.R
@@ -11,7 +11,7 @@
## version (at your option). See the GNU General Public License at
##
vignettes/scaffold.Rmd
scaffold.Rmd
vignettes/usage_template.Rmd
usage_template.Rmd
Xiao S, Moore T, Watt C (2024). msDiaLogue: Analysis + Visuals for Data Indep. Aquisition Mass Spectrometry Data. -R package version 0.0.4, https://github.com/uconn-scs/msDiaLogue. +R package version 0.0.5, https://github.com/uconn-scs/msDiaLogue.
@Manual{, title = {msDiaLogue: Analysis + Visuals for Data Indep. Aquisition Mass Spectrometry Data}, author = {Shiying Xiao and Timothy Moore and Charles Watt}, year = {2024}, - note = {R package version 0.0.4}, + note = {R package version 0.0.5}, url = {https://github.com/uconn-scs/msDiaLogue}, }diff --git a/docs/index.html b/docs/index.html index 6ee4050..5fa8349 100644 --- a/docs/index.html +++ b/docs/index.html @@ -28,7 +28,7 @@ msDiaLogue - 0.0.4 + 0.0.5
"t-test": unequal variance t-test.
"mod.t-test": moderated t-test (Smyth 2004) +
A string (default = "t-test") specifying which statistical test to use:
"t-test": Unequal variance t-test.
"mod.t-test": Moderated t-test (Smyth 2004) .
"MA": output to plot an MA plot.
"MA": Output to plot an MA plot.
"t-test" or "mod.t-test": The differences in means and P-values for each protein -between the two conditions. Note that the differences are calculated by subtracting the -mean of the second condition from the mean of the first condition (Condition 1 - -Condition 2).
"MA": Protein-wise averages within each condition.
The second condition serves as the reference for comparison.
"t-test" and "mod.t-test": The differences are calculated by subtracting +the mean of the second condition from the mean of the first condition (Condition 1 - +Condition 2).
"MA": The rows are ordered by conditions
. Specifically, the first row
+corresponds to the protein-wise average of the first condition, and the second row
+corresponds to the second condition.
The column 'Stat' in the generated data.frame includes the following statistics:
n: number.
mean: mean.
sd: standard deviation.
median: median.
trimmed: trimmed mean with a trim of 0.1.
mad: median absolute deviation (from the median).
min: minimum.
max: maximum.
range: the difference between the maximum and minimum value.
skew: skewness.
kurtosis: kurtosis.
se: standard error.
The column 'Stat' in the generated data.frame includes the following statistics:
n: Number.
mean: Mean.
sd: Standard deviation.
median: Median.
trimmed: Trimmed mean with a trim of 0.1.
mad: Median absolute deviation (from the median).
min: Minimum.
max: Maximum.
range: The difference between the maximum and minimum value.
skew: Skewness.
kurtosis: Kurtosis.
se: Standard error.