diff --git a/Rscript/Library/mzkit_app/@export/xcms.d.ts b/Rscript/Library/mzkit_app/@export/xcms.d.ts index b873301a83..3cdac2bcd9 100644 --- a/Rscript/Library/mzkit_app/@export/xcms.d.ts +++ b/Rscript/Library/mzkit_app/@export/xcms.d.ts @@ -9,6 +9,23 @@ * */ declare namespace xcms { + /** + * cast the xcms find peaks result raw dataframe to mzkit peak feature data + * + * + * @param x A dataframe result of the xcms ``findPeaks``. data could be generated via ``as.data.frame(findPeaks(data));``. + * this raw data frame output contains data fields: + * + * 1. mz, mzmin, mzmax + * 2. rt, rtmin, rtmax + * 3. into, intf + * 4. maxo, maxf + * 5. i + * 6. sn + * @param sample_name + * + default value Is ``null``. + */ + function cast_findpeaks_raw(x: object, sample_name?: string): object; /** * @param group_features default value Is ``false``. * @param env default value Is ``null``. diff --git a/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms.md b/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms.md index 524243fcab..6081bfda2d 100644 --- a/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms.md +++ b/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms.md @@ -3,3 +3,4 @@ the xcms interop and data handler + [parse_xcms_samples](xcms/parse_xcms_samples.1) ++ [cast_findpeaks_raw](xcms/cast_findpeaks_raw.1) cast the xcms find peaks result raw dataframe to mzkit peak feature data diff --git a/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms/cast_findpeaks_raw.1 b/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms/cast_findpeaks_raw.1 new file mode 100644 index 0000000000..95c6389fd0 --- /dev/null +++ b/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms/cast_findpeaks_raw.1 @@ -0,0 +1,31 @@ +.\" man page create by R# package system. +.TH XCMS 1 2000-Jan "cast_findpeaks_raw" "cast_findpeaks_raw" +.SH NAME +cast_findpeaks_raw \- cast the xcms find peaks result raw dataframe to mzkit peak feature data +.SH SYNOPSIS +\fIcast_findpeaks_raw(\fBx\fR as dataframe, +\fBsample_name\fR as string = \fB\fR);\fR +.SH DESCRIPTION +.PP +cast the xcms find peaks result raw dataframe to mzkit peak feature data +.PP +.SH OPTIONS +.PP +\fBx\fB \fR\- + A dataframe result of the xcms \fBfindPeaks\fR. data could be generated via \fBas.data.frame(findPeaks(data));\fR. + this raw data frame output contains data fields: + + 1. mz, mzmin, mzmax + 2. rt, rtmin, rtmax + 3. into, intf + 4. maxo, maxf + 5. i + 6. sn +. +.PP +.SH SEE ALSO +xcms +.SH FILES +.PP +mz_quantify.dll +.PP diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XcmsSamplePeak.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XcmsSamplePeak.html index ee7332f39d..2c482a0e47 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XcmsSamplePeak.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XcmsSamplePeak.html @@ -22,7 +22,7 @@

XcmsSamplePeak

Description

- +

cast findPeaks result to dataframe

Declare

@@ -30,17 +30,30 @@

Declare

# namespace BioNovoGene.Analytical.MassSpectrometry.Math export class XcmsSamplePeak { + # 峰的索引或标识符。 ID: string; + # 峰的峰下面积（峰的积分面积）。 intb: double; + # 峰的总强度（积分强度）。 into: double; + # 峰的最大过滤强度值。 + maxf: double; + # 峰的最大原始强度值。 maxo: double; + # 峰的中心质荷比（m/z）值。 mz: double; + # 峰的最高质荷比（m/z）值。 mzmax: double; + # 峰的最低质荷比（m/z）值。 mzmin: double; + # 峰的中心保留时间（Retention Time，RT）。 rt: double; + # 峰的结束保留时间。 rtmax: double; + # 峰的起始保留时间。 rtmin: double; sample: string; + # 峰的信噪比（Signal-to-Noise ratio）。 sn: double; } diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms.html index 080898e464..751c5b9451 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms.html @@ -86,6 +86,12 @@

xcms

parse_xcms_samples + + + + cast_findpeaks_raw + +

cast the xcms find peaks result raw dataframe to mzkit peak feature data

diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms/cast_findpeaks_raw.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms/cast_findpeaks_raw.html new file mode 100644 index 0000000000..94c0184407 --- /dev/null +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms/cast_findpeaks_raw.html @@ -0,0 +1,79 @@ + + + + + cast the xcms find peaks result raw dataframe to mzkit peak feature data + + + + + + +
+ + + + + + +
cast_findpeaks_raw {xcms}R Documentation
+ +

cast the xcms find peaks result raw dataframe to mzkit peak feature data

+ +

Description

+ + + +

Usage

+ +
+ 
cast_findpeaks_raw(x,
+    sample.name = NULL);
+
+ +

Arguments

+ + + +
x
+

A dataframe result of the xcms findPeaks. data could be generated via as.data.frame(findPeaks(data));. + this raw data frame output contains data fields: + + 1. mz, mzmin, mzmax + 2. rt, rtmin, rtmax + 3. into, intf + 4. maxo, maxf + 5. i + 6. sn. [as dataframe]

+ +
+ + +

Details

+ + + +

Authors

+ + BioNovoGene + +

Value

+ + this function returns data object of type PeakFeature.

clr value class

+ +

Examples

+ + + +
+
[Package xcms version 1.0.0.0 Index] +
+
+ + + + + + + \ No newline at end of file