这个描述gatingML文件演示了如何从Cytobank可以导入导出R作为GatingSet对象。

库(flowWorkspace)库(CytoML) acs < -执行(“extdata / cytobank_experiment。acs”,包= " CytoML”)

创建cytobank_experiment对象从ACS包从Cytobank出口

< - open_cytobank_experiment (acs)

# # # # cytobank实验:tcell gatingML文件:/ tmp / RtmpWSYgTf / file3e213c02ee5c /实验/ 3637 / cytobank_gate_ml2_v41。xml # # # #面板样品1面板1 1

cytobank_experiment是一个包装吗ACS文件,它可以检查不同的访问器。

sampleNames (ce)

# # [1]“CytoTrol_CytoTrol_1.fcs”

colnames (ce)

# # [1]“FSC-A”“FSC-H”“FSC-W”“SSC-A”“B710-A”“R660-A”“R780-A”“V450-A”# # [9]“V545-A”“G560-A”“G780-A”“时间”

markernames (ce)

# # CytoTrol_CytoTrol_1美元。fcs## [1] "FSC-A" "FSC-H" "FSC-W" "SSC-A" "CD4" ## [6] "CD38 APC" "CD8 APCH7" "CD3" "HLA-DR V500" "CCR7 PE" ## [11] "CD45RA PECy7" "Time"

pData (ce)

# # # # CytoTrol_CytoTrol_1个人名字条件。fcs CytoTrol_CytoTrol_1。fcs condition1 ptid1

然后导入cytobank_experiment成GatingSet

gs < - cytobank_to_gatingset (ce)

或者,可以通过进口gatingML和fcsCytobank没有单独下载的文件形式ACS。

美元xmlfile < - ce gatingML fcsFiles < -列表。文件(ce fcsdir美元,full.names = TRUE) gs < - cytobank_to_gatingset (xmlfile fcsFiles)

但是,它没有信息yaml文件的一部分ACS)。如样品标签(即。pData)和定制markernames。所以建议导入ACS。

检查结果

库(ggcyto) # #情节盖茨autoplot (gs [[1]])

#提取人口统计gs_pop_get_count_fast (gs statType =“计数”)

# # # #名人口1:CytoTrol_CytoTrol_1。fcs /没有碎片# # 2:CytoTrol_CytoTrol_1。fcs/not debris/singlets ## 3: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3 ## 4: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3/CD8 ## 5: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3/CD8/CD8_Q2 ## 6: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3/CD4 ## 7: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3/CD4/Q1 ## 8: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3/CD4/Q2 ## 9: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3/CD4/Q4 ## 10: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3/CD4/Q3 ## 11: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3/CD8/CD8_Q2/CD38 range ## 12: CytoTrol_CytoTrol_1.fcs /not debris/singlets/CD3/CD8/CD8_Q2/HLA range ## Parent Count ParentCount ## 1: root 87876 119531 ## 2: /not debris 79845 87876 ## 3: /not debris/singlets 53135 79845 ## 4: /not debris/singlets/CD3 12862 53135 ## 5: /not debris/singlets/CD3/CD8 2331 12862 ## 6: /not debris/singlets/CD3 33653 53135 ## 7: /not debris/singlets/CD3/CD4 419 33653 ## 8: /not debris/singlets/CD3/CD4 11429 33653 ## 9: /not debris/singlets/CD3/CD4 4119 33653 ## 10: /not debris/singlets/CD3/CD4 17686 33653 ## 11: /not debris/singlets/CD3/CD8/CD8_Q2 2331 2331 ## 12: /not debris/singlets/CD3/CD8/CD8_Q2 2315 2331