hello煮甥，大家好道盏，今天我們來總結單細胞數(shù)據(jù)識別腫瘤細胞的分析原理姻灶。其中單細胞識別腫瘤細胞最大的問題在于各聘，reference染坯，什么細胞作為reference算凿，上皮細胞癌變降宅，自然是正常的上皮細胞作為reference喷兼，但很多時候菇绵，光依靠單細胞數(shù)據(jù)我們我們無法區(qū)分惡性和非惡性的細胞類型肄渗，CNV判斷也需要很精準的人為監(jiān)督和數(shù)據(jù)分析，這一次咬最，我們來分析一下識別惡性細胞的分析原理翎嫡。
這里要注意啊，一定要使用配套的單細胞數(shù)據(jù)永乌，確保其中含有惡性的細胞類型惑申，不然光有正常的細胞類型也能分析出結果，拿到的結果是沒有任何用處的翅雏。
大家推斷CNV應該用的是inferCNV或者copycat圈驼，原理都差不多。個人傾向于copycat望几。
CNV Estimation：Initial CNVs (CNV0) were estimated by sorting the analyzed genes by their chromosomal location and applying a moving average to the relative expression values, with a sliding window of 100 genes within each chromosome, 這里大家應該都知道才對绩脆。我們逐步解讀。
第一步：To avoid considerable impact of any particular gene on the moving average, we limited the relative expression values to [-3,3] by replacing all values above 3 by a ceiling of 3, and replacing values below -3 by a floor of -3.（這里不知道大家知道多少橄抹，對數(shù)據(jù)進行剪接,這是必要的）This was performed only in the context of CNV estimation靴迫。
第二步：We scored each cell for the extent of CNV signal, defined as the mean of squares of CNV0 values across the genome, and for the correlation between the CNV0 profile of each cell with the average CNV0 profile of all cells from the corresponding tumor.(這個地方不陌生吧，就是對CNV的判斷)楼誓。
第三步：Putative malignant cells were then defined as those with CNV signal above 0.05 and CNV correlation above 0.5, putative non-malignant cells as those below the two cutoffs, and unresolved cells as those above only one of the thresholds.（跟inferCNV的軟件閾值是一致的）.
第四步：檢驗玉锌，This initial analysis was based on the average CNV0 of all cells as a reference, which is biased due to the inclusion of many malignant cells. We thus redefined CNV estimations, the CNV signal, and CNV correlations values using the average patterns of nonmalignant cells as a reference.（真正的ref必然是相同細胞類型的正常細胞）。
第五步：CNV estimate ：
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當然疟羹，inferCNV軟件還有一步降噪主守，大家感興趣可以多多看看，總結歸納榄融。
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基礎知識参淫，多多學習，生活很好愧杯，有你更好
